Diff for /imach/src/imach.c between versions 1.41.2.2 and 1.148

version 1.41.2.2, 2003/06/13 07:45:28 version 1.148, 2014/06/17 17:38:48
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.148  2014/06/17 17:38:48  brouard
      Summary: Nothing new
   This program computes Healthy Life Expectancies from    Author: Brouard
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Just a new packaging for OS/X version 0.98nS
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.147  2014/06/16 10:33:11  brouard
   second wave of interviews ("longitudinal") which measure each change    *** empty log message ***
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.146  2014/06/16 10:20:28  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: Merge
   Maximum Likelihood of the parameters involved in the model.  The    Author: Brouard
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Merge, before building revised version.
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.145  2014/06/10 21:23:15  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Summary: Debugging with valgrind
   complex model than "constant and age", you should modify the program    Author: Nicolas Brouard
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Lot of changes in order to output the results with some covariates
   convergence.    After the Edimburgh REVES conference 2014, it seems mandatory to
     improve the code.
   The advantage of this computer programme, compared to a simple    No more memory valgrind error but a lot has to be done in order to
   multinomial logistic model, is clear when the delay between waves is not    continue the work of splitting the code into subroutines.
   identical for each individual. Also, if a individual missed an    Also, decodemodel has been improved. Tricode is still not
   intermediate interview, the information is lost, but taken into    optimal. nbcode should be improved. Documentation has been added in
   account using an interpolation or extrapolation.      the source code.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.143  2014/01/26 09:45:38  brouard
   conditional to the observed state i at age x. The delay 'h' can be    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   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    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.142  2014/01/26 03:57:36  brouard
   hPijx.    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   
   Also this programme outputs the covariance matrix of the parameters but also    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.141  2014/01/26 02:42:01  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.140  2011/09/02 10:37:54  brouard
   from the European Union.    Summary: times.h is ok with mingw32 now.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.139  2010/06/14 07:50:17  brouard
   can be accessed at http://euroreves.ined.fr/imach .    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   **********************************************************************/    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
    
 #include <math.h>    Revision 1.138  2010/04/30 18:19:40  brouard
 #include <stdio.h>    *** empty log message ***
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
 #define MAXLINE 256    than V1+V2. A lot of change to be done. Unstable.
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.136  2010/04/26 20:30:53  brouard
 #define FILENAMELENGTH 80    (Module): merging some libgsl code. Fixing computation
 /*#define DEBUG*/    of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
 /*#define windows*/    Some cleaning of code and comments added.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.135  2009/10/29 15:33:14  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.134  2009/10/29 13:18:53  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.133  2009/07/06 10:21:25  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    just nforces
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.132  2009/07/06 08:22:05  brouard
 #define YEARM 12. /* Number of months per year */    Many tings
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
   
 int erreur; /* Error number */    Revision 1.130  2009/05/26 06:44:34  brouard
 int nvar;    (Module): Max Covariate is now set to 20 instead of 8. A
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    lot of cleaning with variables initialized to 0. Trying to make
 int npar=NPARMAX;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.129  2007/08/31 13:49:27  lievre
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    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 popbased=0;  
     Revision 1.128  2006/06/30 13:02:05  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Clarifications on computing e.j
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.127  2006/04/28 18:11:50  brouard
 int mle, weightopt;    (Module): Yes the sum of survivors was wrong since
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    imach-114 because nhstepm was no more computed in the age
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    loop. Now we define nhstepma in the age loop.
 double jmean; /* Mean space between 2 waves */    (Module): In order to speed up (in case of numerous covariates) we
 double **oldm, **newm, **savm; /* Working pointers to matrices */    compute health expectancies (without variances) in a first step
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    and then all the health expectancies with variances or standard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    deviation (needs data from the Hessian matrices) which slows the
 FILE *ficgp,*ficresprob,*ficpop;    computation.
 FILE *ficreseij;    In the future we should be able to stop the program is only health
   char filerese[FILENAMELENGTH];    expectancies and graph are needed without standard deviations.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.126  2006/04/28 17:23:28  brouard
  FILE  *ficresvpl;    (Module): Yes the sum of survivors was wrong since
   char fileresvpl[FILENAMELENGTH];    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 #define NR_END 1    Version 0.98h
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 #define NRANSI    Forecasting file added.
 #define ITMAX 200  
     Revision 1.124  2006/03/22 17:13:53  lievre
 #define TOL 2.0e-4    Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.123  2006/03/20 10:52:43  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    * imach.c (Module): Weights can have a decimal point as for
 #define TINY 1.0e-20    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 static double maxarg1,maxarg2;    Modification of warning when the covariates values are not 0 or
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    1.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Version 0.98g
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.122  2006/03/20 09:45:41  brouard
 #define rint(a) floor(a+0.5)    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 static double sqrarg;    otherwise the weight is truncated).
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Modification of warning when the covariates values are not 0 or
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    1.
     Version 0.98g
 int imx;  
 int stepm;    Revision 1.121  2006/03/16 17:45:01  lievre
 /* Stepm, step in month: minimum step interpolation*/    * imach.c (Module): Comments concerning covariates added
   
 int estepm;    * imach.c (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 1.120  2006/03/16 15:10:38  lievre
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): refinements in the computation of lli if
 double **pmmij, ***probs, ***mobaverage;    status=-2 in order to have more reliable computation if stepm is
 double dateintmean=0;    not 1 month. Version 0.98f
   
 double *weight;    Revision 1.119  2006/03/15 17:42:26  brouard
 int **s; /* Status */    (Module): Bug if status = -2, the loglikelihood was
 double *agedc, **covar, idx;    computed as likelihood omitting the logarithm. Version O.98e
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.118  2006/03/14 18:20:07  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): varevsij Comments added explaining the second
 double ftolhess; /* Tolerance for computing hessian */    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /**************** split *************************/    (Module): Function pstamp added
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Module): Version 0.98d
 {  
    char *s;                             /* pointer */    Revision 1.117  2006/03/14 17:16:22  brouard
    int  l1, l2;                         /* length counters */    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
    l1 = strlen( path );                 /* length of path */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Function pstamp added
 #ifdef windows    (Module): Version 0.98d
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Revision 1.116  2006/03/06 10:29:27  brouard
    s = strrchr( path, '/' );            /* find last / */    (Module): Variance-covariance wrong links and
 #endif    varian-covariance of ej. is needed (Saito).
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.115  2006/02/27 12:17:45  brouard
       extern char       *getwd( );    (Module): One freematrix added in mlikeli! 0.98c
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.114  2006/02/26 12:57:58  brouard
 #else    (Module): Some improvements in processing parameter
       extern char       *getcwd( );    filename with strsep.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.113  2006/02/24 14:20:24  brouard
 #endif    (Module): Memory leaks checks with valgrind and:
          return( GLOCK_ERROR_GETCWD );    datafile was not closed, some imatrix were not freed and on matrix
       }    allocation too.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.112  2006/01/30 09:55:26  brouard
       s++;                              /* after this, the filename */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.111  2006/01/25 20:38:18  brouard
       strcpy( name, s );                /* save file name */    (Module): Lots of cleaning and bugs added (Gompertz)
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): Comments can be added in data file. Missing date values
       dirc[l1-l2] = 0;                  /* add zero */    can be a simple dot '.'.
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.110  2006/01/25 00:51:50  brouard
 #ifdef windows    (Module): Lots of cleaning and bugs added (Gompertz)
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.109  2006/01/24 19:37:15  brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Module): Comments (lines starting with a #) are allowed in data.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.108  2006/01/19 18:05:42  lievre
    s++;    Gnuplot problem appeared...
    strcpy(ext,s);                       /* save extension */    To be fixed
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.107  2006/01/19 16:20:37  brouard
    strncpy( finame, name, l1-l2);    Test existence of gnuplot in imach path
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.106  2006/01/19 13:24:36  brouard
 }    Some cleaning and links added in html output
   
     Revision 1.105  2006/01/05 20:23:19  lievre
 /******************************************/    *** empty log message ***
   
 void replace(char *s, char*t)    Revision 1.104  2005/09/30 16:11:43  lievre
 {    (Module): sump fixed, loop imx fixed, and simplifications.
   int i;    (Module): If the status is missing at the last wave but we know
   int lg=20;    that the person is alive, then we can code his/her status as -2
   i=0;    (instead of missing=-1 in earlier versions) and his/her
   lg=strlen(t);    contributions to the likelihood is 1 - Prob of dying from last
   for(i=0; i<= lg; i++) {    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     (s[i] = t[i]);    the healthy state at last known wave). Version is 0.98
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.103  2005/09/30 15:54:49  lievre
 }    (Module): sump fixed, loop imx fixed, and simplifications.
   
 int nbocc(char *s, char occ)    Revision 1.102  2004/09/15 17:31:30  brouard
 {    Add the possibility to read data file including tab characters.
   int i,j=0;  
   int lg=20;    Revision 1.101  2004/09/15 10:38:38  brouard
   i=0;    Fix on curr_time
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.100  2004/07/12 18:29:06  brouard
   if  (s[i] == occ ) j++;    Add version for Mac OS X. Just define UNIX in Makefile
   }  
   return j;    Revision 1.99  2004/06/05 08:57:40  brouard
 }    *** empty log message ***
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.98  2004/05/16 15:05:56  brouard
 {    New version 0.97 . First attempt to estimate force of mortality
   int i,lg,j,p=0;    directly from the data i.e. without the need of knowing the health
   i=0;    state at each age, but using a Gompertz model: log u =a + b*age .
   for(j=0; j<=strlen(t)-1; j++) {    This is the basic analysis of mortality and should be done before any
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    other analysis, in order to test if the mortality estimated from the
   }    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
   lg=strlen(t);  
   for(j=0; j<p; j++) {    The same imach parameter file can be used but the option for mle should be -3.
     (u[j] = t[j]);  
   }    Agnès, who wrote this part of the code, tried to keep most of the
      u[p]='\0';    former routines in order to include the new code within the former code.
   
    for(j=0; j<= lg; j++) {    The output is very simple: only an estimate of the intercept and of
     if (j>=(p+1))(v[j-p-1] = t[j]);    the slope with 95% confident intervals.
   }  
 }    Current limitations:
     A) Even if you enter covariates, i.e. with the
 /********************** nrerror ********************/    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
 void nrerror(char error_text[])  
 {    Revision 1.97  2004/02/20 13:25:42  lievre
   fprintf(stderr,"ERREUR ...\n");    Version 0.96d. Population forecasting command line is (temporarily)
   fprintf(stderr,"%s\n",error_text);    suppressed.
   exit(1);  
 }    Revision 1.96  2003/07/15 15:38:55  brouard
 /*********************** vector *******************/    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 double *vector(int nl, int nh)    rewritten within the same printf. Workaround: many printfs.
 {  
   double *v;    Revision 1.95  2003/07/08 07:54:34  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    * imach.c (Repository):
   if (!v) nrerror("allocation failure in vector");    (Repository): Using imachwizard code to output a more meaningful covariance
   return v-nl+NR_END;    matrix (cov(a12,c31) instead of numbers.
 }  
     Revision 1.94  2003/06/27 13:00:02  brouard
 /************************ free vector ******************/    Just cleaning
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.93  2003/06/25 16:33:55  brouard
   free((FREE_ARG)(v+nl-NR_END));    (Module): On windows (cygwin) function asctime_r doesn't
 }    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.92  2003/06/25 16:30:45  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   int *v;    exist so I changed back to asctime which exists.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.91  2003/06/25 15:30:29  brouard
   return v-nl+NR_END;    * imach.c (Repository): Duplicated warning errors corrected.
 }    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 /******************free ivector **************************/    is stamped in powell.  We created a new html file for the graphs
 void free_ivector(int *v, long nl, long nh)    concerning matrix of covariance. It has extension -cov.htm.
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.90  2003/06/24 12:34:15  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /******************* 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 1.89  2003/06/24 12:30:52  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    mle=-1 a template is output in file "or"mypar.txt with the design
   int **m;    of the covariance matrix to be input.
    
   /* allocate pointers to rows */    Revision 1.88  2003/06/23 17:54:56  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    * 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.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.87  2003/06/18 12:26:01  brouard
   m -= nrl;    Version 0.96
    
      Revision 1.86  2003/06/17 20:04:08  brouard
   /* allocate rows and set pointers to them */    (Module): Change position of html and gnuplot routines and added
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    routine fileappend.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.85  2003/06/17 13:12:43  brouard
   m[nrl] -= ncl;    * imach.c (Repository): Check when date of death was earlier that
      current date of interview. It may happen when the death was just
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    prior to the death. In this case, dh was negative and likelihood
      was wrong (infinity). We still send an "Error" but patch by
   /* return pointer to array of pointers to rows */    assuming that the date of death was just one stepm after the
   return m;    interview.
 }    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
 /****************** free_imatrix *************************/    memory allocation. But we also truncated to 8 characters (left
 void free_imatrix(m,nrl,nrh,ncl,nch)    truncation)
       int **m;    (Repository): No more line truncation errors.
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.84  2003/06/13 21:44:43  brouard
 {    * imach.c (Repository): Replace "freqsummary" at a correct
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    place. It differs from routine "prevalence" which may be called
   free((FREE_ARG) (m+nrl-NR_END));    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  */
   m += NR_END;  /*
   m -= nrl;     Interpolated Markov Chain
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Short summary of the programme:
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    This program computes Healthy Life Expectancies from
   m[nrl] -= ncl;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    interviewed on their health status or degree of disability (in the
   return m;    case of a health survey which is our main interest) -2- at least a
 }    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 /*************************free matrix ************************/    computed from the time spent in each health state according to a
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    model. More health states you consider, more time is necessary to reach the
 {    Maximum Likelihood of the parameters involved in the model.  The
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    simplest model is the multinomial logistic model where pij is the
   free((FREE_ARG)(m+nrl-NR_END));    probability to be observed in state j at the second wave
 }    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 /******************* ma3x *******************************/    'age' is age and 'sex' is a covariate. If you want to have a more
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    complex model than "constant and age", you should modify the program
 {    where the markup *Covariates have to be included here again* invites
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    you to do it.  More covariates you add, slower the
   double ***m;    convergence.
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    The advantage of this computer programme, compared to a simple
   if (!m) nrerror("allocation failure 1 in matrix()");    multinomial logistic model, is clear when the delay between waves is not
   m += NR_END;    identical for each individual. Also, if a individual missed an
   m -= nrl;    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    hPijx is the probability to be observed in state i at age x+h
   m[nrl] += NR_END;    conditional to the observed state i at age x. The delay 'h' can be
   m[nrl] -= ncl;    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    and the contribution of each individual to the likelihood is simply
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    hPijx.
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Also this programme outputs the covariance matrix of the parameters but also
   for (j=ncl+1; j<=nch; j++)    of the life expectancies. It also computes the period (stable) prevalence. 
     m[nrl][j]=m[nrl][j-1]+nlay;    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   for (i=nrl+1; i<=nrh; i++) {             Institut national d'études démographiques, Paris.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    This software have been partly granted by Euro-REVES, a concerted action
     for (j=ncl+1; j<=nch; j++)    from the European Union.
       m[i][j]=m[i][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
   return m;    can be accessed at http://euroreves.ined.fr/imach .
 }  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 /*************************free ma3x ************************/    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    
 {    **********************************************************************/
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /*
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    main
   free((FREE_ARG)(m+nrl-NR_END));    read parameterfile
 }    read datafile
     concatwav
 /***************** f1dim *************************/    freqsummary
 extern int ncom;    if (mle >= 1)
 extern double *pcom,*xicom;      mlikeli
 extern double (*nrfunc)(double []);    print results files
      if mle==1 
 double f1dim(double x)       computes hessian
 {    read end of parameter file: agemin, agemax, bage, fage, estepm
   int j;        begin-prev-date,...
   double f;    open gnuplot file
   double *xt;    open html file
      period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   xt=vector(1,ncom);     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   f=(*nrfunc)(xt);      freexexit2 possible for memory heap.
   free_vector(xt,1,ncom);  
   return f;    h Pij x                         | pij_nom  ficrestpij
 }     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
          1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
 /*****************brent *************************/         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   int iter;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   double a,b,d,etemp;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   double fu,fv,fw,fx;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   double ftemp;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    forecasting if prevfcast==1 prevforecast call prevalence()
      health expectancies
   a=(ax < cx ? ax : cx);    Variance-covariance of DFLE
   b=(ax > cx ? ax : cx);    prevalence()
   x=w=v=bx;     movingaverage()
   fw=fv=fx=(*f)(x);    varevsij() 
   for (iter=1;iter<=ITMAX;iter++) {    if popbased==1 varevsij(,popbased)
     xm=0.5*(a+b);    total life expectancies
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    Variance of period (stable) prevalence
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/   end
     printf(".");fflush(stdout);  */
 #ifdef DEBUG  
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif   
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #include <math.h>
       *xmin=x;  #include <stdio.h>
       return fx;  #include <stdlib.h>
     }  #include <string.h>
     ftemp=fu;  #include <unistd.h>
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  #include <limits.h>
       q=(x-v)*(fx-fw);  #include <sys/types.h>
       p=(x-v)*q-(x-w)*r;  #include <sys/stat.h>
       q=2.0*(q-r);  #include <errno.h>
       if (q > 0.0) p = -p;  extern int errno;
       q=fabs(q);  
       etemp=e;  #ifdef LINUX
       e=d;  #include <time.h>
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #include "timeval.h"
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #else
       else {  #include <sys/time.h>
         d=p/q;  #endif
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  #ifdef GSL
           d=SIGN(tol1,xm-x);  #include <gsl/gsl_errno.h>
       }  #include <gsl/gsl_multimin.h>
     } else {  #endif
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  /* #include <libintl.h> */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /* #define _(String) gettext (String) */
     fu=(*f)(u);  
     if (fu <= fx) {  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  #define GNUPLOTPROGRAM "gnuplot"
         SHFT(fv,fw,fx,fu)  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         } else {  #define FILENAMELENGTH 132
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
             v=w;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
             w=u;  
             fv=fw;  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
             fw=fu;  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  #define NINTERVMAX 8
             fv=fu;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
           }  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
         }  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   }  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   nrerror("Too many iterations in brent");  #define MAXN 20000
   *xmin=x;  #define YEARM 12. /**< Number of months per year */
   return fx;  #define AGESUP 130
 }  #define AGEBASE 40
   #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
 /****************** mnbrak ***********************/  #ifdef UNIX
   #define DIRSEPARATOR '/'
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define CHARSEPARATOR "/"
             double (*func)(double))  #define ODIRSEPARATOR '\\'
 {  #else
   double ulim,u,r,q, dum;  #define DIRSEPARATOR '\\'
   double fu;  #define CHARSEPARATOR "\\"
    #define ODIRSEPARATOR '/'
   *fa=(*func)(*ax);  #endif
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  /* $Id$ */
     SHFT(dum,*ax,*bx,dum)  /* $State$ */
       SHFT(dum,*fb,*fa,dum)  
       }  char version[]="Imach version 0.98nS, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   *cx=(*bx)+GOLD*(*bx-*ax);  char fullversion[]="$Revision$ $Date$"; 
   *fc=(*func)(*cx);  char strstart[80];
   while (*fb > *fc) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
     r=(*bx-*ax)*(*fb-*fc);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     q=(*bx-*cx)*(*fb-*fa);  int nvar=0, nforce=0; /* Number of variables, number of forces */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     if ((*bx-u)*(u-*cx) > 0.0) {  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       fu=(*func)(u);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       fu=(*func)(u);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       if (fu < *fc) {  int cptcov=0; /* Working variable */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int npar=NPARMAX;
           SHFT(*fb,*fc,fu,(*func)(u))  int nlstate=2; /* Number of live states */
           }  int ndeath=1; /* Number of dead states */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       u=ulim;  int popbased=0;
       fu=(*func)(u);  
     } else {  int *wav; /* Number of waves for this individuual 0 is possible */
       u=(*cx)+GOLD*(*cx-*bx);  int maxwav=0; /* Maxim number of waves */
       fu=(*func)(u);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     }  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     SHFT(*ax,*bx,*cx,u)  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       SHFT(*fa,*fb,*fc,fu)                     to the likelihood and the sum of weights (done by funcone)*/
       }  int mle=1, weightopt=0;
 }  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 */
 /*************** linmin ************************/  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int ncom;  double jmean=1; /* Mean space between 2 waves */
 double *pcom,*xicom;  double **matprod2(); /* test */
 double (*nrfunc)(double []);  double **oldm, **newm, **savm; /* Working pointers to matrices */
    double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /*FILE *fic ; */ /* Used in readdata only */
 {  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   double brent(double ax, double bx, double cx,  FILE *ficlog, *ficrespow;
                double (*f)(double), double tol, double *xmin);  int globpr=0; /* Global variable for printing or not */
   double f1dim(double x);  double fretone; /* Only one call to likelihood */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  long ipmx=0; /* Number of contributions */
               double *fc, double (*func)(double));  double sw; /* Sum of weights */
   int j;  char filerespow[FILENAMELENGTH];
   double xx,xmin,bx,ax;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double fx,fb,fa;  FILE *ficresilk;
    FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   ncom=n;  FILE *ficresprobmorprev;
   pcom=vector(1,n);  FILE *fichtm, *fichtmcov; /* Html File */
   xicom=vector(1,n);  FILE *ficreseij;
   nrfunc=func;  char filerese[FILENAMELENGTH];
   for (j=1;j<=n;j++) {  FILE *ficresstdeij;
     pcom[j]=p[j];  char fileresstde[FILENAMELENGTH];
     xicom[j]=xi[j];  FILE *ficrescveij;
   }  char filerescve[FILENAMELENGTH];
   ax=0.0;  FILE  *ficresvij;
   xx=1.0;  char fileresv[FILENAMELENGTH];
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  FILE  *ficresvpl;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  char fileresvpl[FILENAMELENGTH];
 #ifdef DEBUG  char title[MAXLINE];
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #endif  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   for (j=1;j<=n;j++) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     xi[j] *= xmin;  char command[FILENAMELENGTH];
     p[j] += xi[j];  int  outcmd=0;
   }  
   free_vector(xicom,1,n);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   free_vector(pcom,1,n);  
 }  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 /*************** powell ************************/  char fileregp[FILENAMELENGTH];
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  char popfile[FILENAMELENGTH];
             double (*func)(double []))  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   int i,ibig,j;  struct timezone tzp;
   double del,t,*pt,*ptt,*xit;  extern int gettimeofday();
   double fp,fptt;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double *xits;  long time_value;
   pt=vector(1,n);  extern long time();
   ptt=vector(1,n);  char strcurr[80], strfor[80];
   xit=vector(1,n);  
   xits=vector(1,n);  char *endptr;
   *fret=(*func)(p);  long lval;
   for (j=1;j<=n;j++) pt[j]=p[j];  double dval;
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  #define NR_END 1
     ibig=0;  #define FREE_ARG char*
     del=0.0;  #define FTOL 1.0e-10
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  #define NRANSI 
       printf(" %d %.12f",i, p[i]);  #define ITMAX 200 
     printf("\n");  
     for (i=1;i<=n;i++) {  #define TOL 2.0e-4 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  #define CGOLD 0.3819660 
 #ifdef DEBUG  #define ZEPS 1.0e-10 
       printf("fret=%lf \n",*fret);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #endif  
       printf("%d",i);fflush(stdout);  #define GOLD 1.618034 
       linmin(p,xit,n,fret,func);  #define GLIMIT 100.0 
       if (fabs(fptt-(*fret)) > del) {  #define TINY 1.0e-20 
         del=fabs(fptt-(*fret));  
         ibig=i;  static double maxarg1,maxarg2;
       }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #ifdef DEBUG  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       printf("%d %.12e",i,(*fret));    
       for (j=1;j<=n;j++) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #define rint(a) floor(a+0.5)
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  static double sqrarg;
       for(j=1;j<=n;j++)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         printf(" p=%.12e",p[j]);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       printf("\n");  int agegomp= AGEGOMP;
 #endif  
     }  int imx; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  int stepm=1;
 #ifdef DEBUG  /* Stepm, step in month: minimum step interpolation*/
       int k[2],l;  
       k[0]=1;  int estepm;
       k[1]=-1;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  int m,nb;
         printf(" %.12e",p[j]);  long *num;
       printf("\n");  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       for(l=0;l<=1;l++) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         for (j=1;j<=n;j++) {  double **pmmij, ***probs;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double *ageexmed,*agecens;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  double dateintmean=0;
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  double *weight;
       }  int **s; /* Status */
 #endif  double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                     * covar=matrix(0,NCOVMAX,1,n); 
       free_vector(xit,1,n);                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       free_vector(xits,1,n);  double  idx; 
       free_vector(ptt,1,n);  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       free_vector(pt,1,n);  int *Ndum; /** Freq of modality (tricode */
       return;  int **codtab; /**< codtab=imatrix(1,100,1,10); */
     }  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  double *lsurv, *lpop, *tpop;
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
       xit[j]=p[j]-pt[j];  double ftolhess; /**< Tolerance for computing hessian */
       pt[j]=p[j];  
     }  /**************** split *************************/
     fptt=(*func)(ptt);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     if (fptt < fp) {  {
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       if (t < 0.0) {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         linmin(p,xit,n,fret,func);    */ 
         for (j=1;j<=n;j++) {    char  *ss;                            /* pointer */
           xi[j][ibig]=xi[j][n];    int   l1, l2;                         /* length counters */
           xi[j][n]=xit[j];  
         }    l1 = strlen(path );                   /* length of path */
 #ifdef DEBUG    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         for(j=1;j<=n;j++)    if ( ss == NULL ) {                   /* no directory, so determine current directory */
           printf(" %.12e",xit[j]);      strcpy( name, path );               /* we got the fullname name because no directory */
         printf("\n");      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 #endif        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       }      /* get current working directory */
     }      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 }        return( GLOCK_ERROR_GETCWD );
       }
 /**** Prevalence limit ****************/      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      l2 = strlen( ss );                  /* length of filename */
      matrix by transitions matrix until convergence is reached */      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
   int i, ii,j,k;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   double min, max, maxmin, maxmax,sumnew=0.;      dirc[l1-l2] = 0;                    /* add zero */
   double **matprod2();      printf(" DIRC2 = %s \n",dirc);
   double **out, cov[NCOVMAX], **pmij();    }
   double **newm;    /* We add a separator at the end of dirc if not exists */
   double agefin, delaymax=50 ; /* Max number of years to converge */    l1 = strlen( dirc );                  /* length of directory */
     if( dirc[l1-1] != DIRSEPARATOR ){
   for (ii=1;ii<=nlstate+ndeath;ii++)      dirc[l1] =  DIRSEPARATOR;
     for (j=1;j<=nlstate+ndeath;j++){      dirc[l1+1] = 0; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf(" DIRC3 = %s \n",dirc);
     }    }
     ss = strrchr( name, '.' );            /* find last / */
    cov[1]=1.;    if (ss >0){
        ss++;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      strcpy(ext,ss);                     /* save extension */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      l1= strlen( name);
     newm=savm;      l2= strlen(ss)+1;
     /* Covariates have to be included here again */      strncpy( finame, name, l1-l2);
      cov[2]=agefin;      finame[l1-l2]= 0;
      }
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    return( 0 );                          /* we're done */
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  }
       }  
       for (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]]];  
   void replace_back_to_slash(char *s, char*t)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    int i;
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    int lg=0;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    i=0;
     lg=strlen(t);
     savm=oldm;    for(i=0; i<= lg; i++) {
     oldm=newm;      (s[i] = t[i]);
     maxmax=0.;      if (t[i]== '\\') s[i]='/';
     for(j=1;j<=nlstate;j++){    }
       min=1.;  }
       max=0.;  
       for(i=1; i<=nlstate; i++) {  char *trimbb(char *out, char *in)
         sumnew=0;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    char *s;
         prlim[i][j]= newm[i][j]/(1-sumnew);    s=out;
         max=FMAX(max,prlim[i][j]);    while (*in != '\0'){
         min=FMIN(min,prlim[i][j]);      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       }        in++;
       maxmin=max-min;      }
       maxmax=FMAX(maxmax,maxmin);      *out++ = *in++;
     }    }
     if(maxmax < ftolpl){    *out='\0';
       return prlim;    return s;
     }  }
   }  
 }  char *cutl(char *blocc, char *alocc, char *in, char occ)
   {
 /*************** transition probabilities ***************/    /* 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')
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )       gives blocc="abcdef2ghi" and alocc="j".
 {       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   double s1, s2;    */
   /*double t34;*/    char *s, *t, *bl;
   int i,j,j1, nc, ii, jj;    t=in;s=in;
     while ((*in != occ) && (*in != '\0')){
     for(i=1; i<= nlstate; i++){      *alocc++ = *in++;
     for(j=1; j<i;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if( *in == occ){
         /*s2 += param[i][j][nc]*cov[nc];*/      *(alocc)='\0';
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      s=++in;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    }
       }   
       ps[i][j]=s2;    if (s == t) {/* occ not found */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      *(alocc-(in-s))='\0';
     }      in=s;
     for(j=i+1; j<=nlstate+ndeath;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    while ( *in != '\0'){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      *blocc++ = *in++;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    }
       }  
       ps[i][j]=s2;    *blocc='\0';
     }    return t;
   }  }
     /*ps[3][2]=1;*/  char *cutv(char *blocc, char *alocc, char *in, char occ)
   {
   for(i=1; i<= nlstate; i++){    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
      s1=0;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     for(j=1; j<i; j++)       gives blocc="abcdef2ghi" and alocc="j".
       s1+=exp(ps[i][j]);       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     for(j=i+1; j<=nlstate+ndeath; j++)    */
       s1+=exp(ps[i][j]);    char *s, *t;
     ps[i][i]=1./(s1+1.);    t=in;s=in;
     for(j=1; j<i; j++)    while (*in != '\0'){
       ps[i][j]= exp(ps[i][j])*ps[i][i];      while( *in == occ){
     for(j=i+1; j<=nlstate+ndeath; j++)        *blocc++ = *in++;
       ps[i][j]= exp(ps[i][j])*ps[i][i];        s=in;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      }
   } /* end i */      *blocc++ = *in++;
     }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    if (s == t) /* occ not found */
     for(jj=1; jj<= nlstate+ndeath; jj++){      *(blocc-(in-s))='\0';
       ps[ii][jj]=0;    else
       ps[ii][ii]=1;      *(blocc-(in-s)-1)='\0';
     }    in=s;
   }    while ( *in != '\0'){
       *alocc++ = *in++;
     }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){    *alocc='\0';
      printf("%lf ",ps[ii][jj]);    return s;
    }  }
     printf("\n ");  
     }  int nbocc(char *s, char occ)
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    int i,j=0;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    int lg=20;
   goto end;*/    i=0;
     return ps;    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /**************** Product of 2 matrices ******************/    }
     return j;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /* void cutv(char *u,char *v, char*t, char occ) */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /* { */
   /* in, b, out are matrice of pointers which should have been initialized  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
      before: only the contents of out is modified. The function returns  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
      a pointer to pointers identical to out */  /*      gives u="abcdef2ghi" and v="j" *\/ */
   long i, j, k;  /*   int i,lg,j,p=0; */
   for(i=nrl; i<= nrh; i++)  /*   i=0; */
     for(k=ncolol; k<=ncoloh; k++)  /*   lg=strlen(t); */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /*   for(j=0; j<=lg-1; j++) { */
         out[i][k] +=in[i][j]*b[j][k];  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*   } */
   return out;  
 }  /*   for(j=0; j<p; j++) { */
   /*     (u[j] = t[j]); */
   /*   } */
 /************* Higher Matrix Product ***************/  /*      u[p]='\0'; */
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /*    for(j=0; j<= lg; j++) { */
 {  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /*   } */
      duration (i.e. until  /* } */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  /********************** nrerror ********************/
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  void nrerror(char error_text[])
      included manually here.  {
     fprintf(stderr,"ERREUR ...\n");
      */    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   int i, j, d, h, k;  }
   double **out, cov[NCOVMAX];  /*********************** vector *******************/
   double **newm;  double *vector(int nl, int nh)
   {
   /* Hstepm could be zero and should return the unit matrix */    double *v;
   for (i=1;i<=nlstate+ndeath;i++)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     for (j=1;j<=nlstate+ndeath;j++){    if (!v) nrerror("allocation failure in vector");
       oldm[i][j]=(i==j ? 1.0 : 0.0);    return v-nl+NR_END;
       po[i][j][0]=(i==j ? 1.0 : 0.0);  }
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /************************ free vector ******************/
   for(h=1; h <=nhstepm; h++){  void free_vector(double*v, int nl, int nh)
     for(d=1; d <=hstepm; d++){  {
       newm=savm;    free((FREE_ARG)(v+nl-NR_END));
       /* Covariates have to be included here again */  }
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /************************ivector *******************************/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int *ivector(long nl,long nh)
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int *v;
       for (k=1; k<=cptcovprod;k++)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /******************free ivector **************************/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  void free_ivector(int *v, long nl, long nh)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  {
       savm=oldm;    free((FREE_ARG)(v+nl-NR_END));
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /************************lvector *******************************/
       for(j=1;j<=nlstate+ndeath;j++) {  long *lvector(long nl,long nh)
         po[i][j][h]=newm[i][j];  {
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    long *v;
          */    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       }    if (!v) nrerror("allocation failure in ivector");
   } /* end h */    return v-nl+NR_END;
   return po;  }
 }  
   /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
 /*************** log-likelihood *************/  {
 double func( double *x)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /******************* imatrix *******************************/
   double **out;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double sw; /* Sum of weights */       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   double lli; /* Individual log likelihood */  { 
   int s1, s2;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   long ipmx;    int **m; 
   /*extern weight */    
   /* We are differentiating ll according to initial status */    /* allocate pointers to rows */ 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   /*for(i=1;i<imx;i++)    if (!m) nrerror("allocation failure 1 in matrix()"); 
     printf(" %d\n",s[4][i]);    m += NR_END; 
   */    m -= nrl; 
   cov[1]=1.;    
     
   for(k=1; k<=nlstate; k++) ll[k]=0.;    /* allocate rows and set pointers to them */ 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for(mi=1; mi<= wav[i]-1; mi++){    m[nrl] += NR_END; 
       for (ii=1;ii<=nlstate+ndeath;ii++)    m[nrl] -= ncl; 
         for (j=1;j<=nlstate+ndeath;j++){    
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
           savm[ii][j]=(ii==j ? 1.0 : 0.0);    
         }    /* return pointer to array of pointers to rows */ 
       for(d=0; d<dh[mi][i]; d++){    return m; 
         newm=savm;  } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  /****************** free_imatrix *************************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  void free_imatrix(m,nrl,nrh,ncl,nch)
         }        int **m;
                long nch,ncl,nrh,nrl; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       /* free an int matrix allocated by imatrix() */ 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  { 
         savm=oldm;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         oldm=newm;    free((FREE_ARG) (m+nrl-NR_END)); 
          } 
          
       } /* end mult */  /******************* matrix *******************************/
        double **matrix(long nrl, long nrh, long ncl, long nch)
       s1=s[mw[mi][i]][i];  {
       s2=s[mw[mi+1][i]][i];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       if( s2 > nlstate){    double **m;
         /* i.e. if s2 is a death state and if the date of death is known then the contribution  
            to the likelihood is the probability to die between last step unit time and current    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
            step unit time, which is also the differences between probability to die before dh    if (!m) nrerror("allocation failure 1 in matrix()");
            and probability to die before dh-stepm .    m += NR_END;
            In version up to 0.92 likelihood was computed    m -= nrl;
            as if date of death was unknown. Death was treated as any other  
            health state: the date of the interview describes the actual state    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
            and not the date of a change in health state. The former idea was    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
            to consider that at each interview the state was recorded    m[nrl] += NR_END;
            (healthy, disable or death) and IMaCh was corrected; but when we    m[nrl] -= ncl;
            introduced the exact date of death then we should have modified  
            the contribution of an exact death to the likelihood. This new    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
            contribution is smaller and very dependent of the step unit    return m;
            stepm. It is no more the probability to die between last interview    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
            and month of death but the probability to survive from last  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
            interview up to one month before death multiplied by the  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
            probability to die within a month. Thanks to Chris     */
            Jackson for correcting this bug.  Former versions increased  }
            mortality artificially. The bad side is that we add another loop  
            which slows down the processing. The difference can be up to 10%  /*************************free matrix ************************/
            lower mortality.  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         */  {
         lli=log(out[s1][s2] - savm[s1][s2]);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       }else{    free((FREE_ARG)(m+nrl-NR_END));
         lli=log(out[s1][s2]); /* or     lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); */  }
         /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       }  /******************* ma3x *******************************/
       ipmx +=1;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       sw += weight[i];  {
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d lli=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],lli,weight[i],out[s1][s2],savm[s1][s2]);*/    double ***m;
     } /* end of wave */  
   } /* end of individual */    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    m += NR_END;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    m -= nrl;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   /*exit(0);*/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   return -l;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
   
 /*********** Maximum Likelihood Estimation ***************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   int i,j, iter;    m[nrl][ncl] += NR_END;
   double **xi,*delti;    m[nrl][ncl] -= nll;
   double fret;    for (j=ncl+1; j<=nch; j++) 
   xi=matrix(1,npar,1,npar);      m[nrl][j]=m[nrl][j-1]+nlay;
   for (i=1;i<=npar;i++)    
     for (j=1;j<=npar;j++)    for (i=nrl+1; i<=nrh; i++) {
       xi[i][j]=(i==j ? 1.0 : 0.0);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   printf("Powell\n");      for (j=ncl+1; j<=nch; j++) 
   powell(p,xi,npar,ftol,&iter,&fret,func);        m[i][j]=m[i][j-1]+nlay;
     }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    return m; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 }    */
   }
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*************************free ma3x ************************/
 {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double  **a,**y,*x,pd;  {
   double **hess;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   int i, j,jk;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int *indx;    free((FREE_ARG)(m+nrl-NR_END));
   }
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  /*************** function subdirf ***********/
   void lubksb(double **a, int npar, int *indx, double b[]) ;  char *subdirf(char fileres[])
   void ludcmp(double **a, int npar, int *indx, double *d) ;  {
     /* Caution optionfilefiname is hidden */
   hess=matrix(1,npar,1,npar);    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
   printf("\nCalculation of the hessian matrix. Wait...\n");    strcat(tmpout,fileres);
   for (i=1;i<=npar;i++){    return tmpout;
     printf("%d",i);fflush(stdout);  }
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  /*************** function subdirf2 ***********/
     /*printf(" %lf ",hess[i][i]);*/  char *subdirf2(char fileres[], char *preop)
   }  {
      
   for (i=1;i<=npar;i++) {    /* Caution optionfilefiname is hidden */
     for (j=1;j<=npar;j++)  {    strcpy(tmpout,optionfilefiname);
       if (j>i) {    strcat(tmpout,"/");
         printf(".%d%d",i,j);fflush(stdout);    strcat(tmpout,preop);
         hess[i][j]=hessij(p,delti,i,j);    strcat(tmpout,fileres);
         hess[j][i]=hess[i][j];        return tmpout;
         /*printf(" %lf ",hess[i][j]);*/  }
       }  
     }  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
   printf("\n");  {
     
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    /* Caution optionfilefiname is hidden */
      strcpy(tmpout,optionfilefiname);
   a=matrix(1,npar,1,npar);    strcat(tmpout,"/");
   y=matrix(1,npar,1,npar);    strcat(tmpout,preop);
   x=vector(1,npar);    strcat(tmpout,preop2);
   indx=ivector(1,npar);    strcat(tmpout,fileres);
   for (i=1;i<=npar;i++)    return tmpout;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /***************** f1dim *************************/
   for (j=1;j<=npar;j++) {  extern int ncom; 
     for (i=1;i<=npar;i++) x[i]=0;  extern double *pcom,*xicom;
     x[j]=1;  extern double (*nrfunc)(double []); 
     lubksb(a,npar,indx,x);   
     for (i=1;i<=npar;i++){  double f1dim(double x) 
       matcov[i][j]=x[i];  { 
     }    int j; 
   }    double f;
     double *xt; 
   printf("\n#Hessian matrix#\n");   
   for (i=1;i<=npar;i++) {    xt=vector(1,ncom); 
     for (j=1;j<=npar;j++) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       printf("%.3e ",hess[i][j]);    f=(*nrfunc)(xt); 
     }    free_vector(xt,1,ncom); 
     printf("\n");    return f; 
   }  } 
   
   /* Recompute Inverse */  /*****************brent *************************/
   for (i=1;i<=npar;i++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  { 
   ludcmp(a,npar,indx,&pd);    int iter; 
     double a,b,d,etemp;
   /*  printf("\n#Hessian matrix recomputed#\n");    double fu,fv,fw,fx;
     double ftemp;
   for (j=1;j<=npar;j++) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     for (i=1;i<=npar;i++) x[i]=0;    double e=0.0; 
     x[j]=1;   
     lubksb(a,npar,indx,x);    a=(ax < cx ? ax : cx); 
     for (i=1;i<=npar;i++){    b=(ax > cx ? ax : cx); 
       y[i][j]=x[i];    x=w=v=bx; 
       printf("%.3e ",y[i][j]);    fw=fv=fx=(*f)(x); 
     }    for (iter=1;iter<=ITMAX;iter++) { 
     printf("\n");      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);
   free_matrix(a,1,npar,1,npar);      fprintf(ficlog,".");fflush(ficlog);
   free_matrix(y,1,npar,1,npar);  #ifdef DEBUG
   free_vector(x,1,npar);      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);
   free_ivector(indx,1,npar);      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);
   free_matrix(hess,1,npar,1,npar);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 }        *xmin=x; 
         return fx; 
 /*************** hessian matrix ****************/      } 
 double hessii( double x[], double delta, int theta, double delti[])      ftemp=fu;
 {      if (fabs(e) > tol1) { 
   int i;        r=(x-w)*(fx-fv); 
   int l=1, lmax=20;        q=(x-v)*(fx-fw); 
   double k1,k2;        p=(x-v)*q-(x-w)*r; 
   double p2[NPARMAX+1];        q=2.0*(q-r); 
   double res;        if (q > 0.0) p = -p; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        q=fabs(q); 
   double fx;        etemp=e; 
   int k=0,kmax=10;        e=d; 
   double l1;        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)); 
   fx=func(x);        else { 
   for (i=1;i<=npar;i++) p2[i]=x[i];          d=p/q; 
   for(l=0 ; l <=lmax; l++){          u=x+d; 
     l1=pow(10,l);          if (u-a < tol2 || b-u < tol2) 
     delts=delt;            d=SIGN(tol1,xm-x); 
     for(k=1 ; k <kmax; k=k+1){        } 
       delt = delta*(l1*k);      } else { 
       p2[theta]=x[theta] +delt;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       k1=func(p2)-fx;      } 
       p2[theta]=x[theta]-delt;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       k2=func(p2)-fx;      fu=(*f)(u); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */      if (fu <= fx) { 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        if (u >= x) a=x; else b=x; 
              SHFT(v,w,x,u) 
 #ifdef DEBUG          SHFT(fv,fw,fx,fu) 
       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);          } else { 
 #endif            if (u < x) a=u; else b=u; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            if (fu <= fw || w == x) { 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){              v=w; 
         k=kmax;              w=u; 
       }              fv=fw; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */              fw=fu; 
         k=kmax; l=lmax*10.;            } else if (fu <= fv || v == x || v == w) { 
       }              v=u; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){              fv=fu; 
         delts=delt;            } 
       }          } 
     }    } 
   }    nrerror("Too many iterations in brent"); 
   delti[theta]=delts;    *xmin=x; 
   return res;    return fx; 
    } 
 }  
   /****************** mnbrak ***********************/
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   int i;              double (*func)(double)) 
   int l=1, l1, lmax=20;  { 
   double k1,k2,k3,k4,res,fx;    double ulim,u,r,q, dum;
   double p2[NPARMAX+1];    double fu; 
   int k;   
     *fa=(*func)(*ax); 
   fx=func(x);    *fb=(*func)(*bx); 
   for (k=1; k<=2; k++) {    if (*fb > *fa) { 
     for (i=1;i<=npar;i++) p2[i]=x[i];      SHFT(dum,*ax,*bx,dum) 
     p2[thetai]=x[thetai]+delti[thetai]/k;        SHFT(dum,*fb,*fa,dum) 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        } 
     k1=func(p2)-fx;    *cx=(*bx)+GOLD*(*bx-*ax); 
      *fc=(*func)(*cx); 
     p2[thetai]=x[thetai]+delti[thetai]/k;    while (*fb > *fc) { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      r=(*bx-*ax)*(*fb-*fc); 
     k2=func(p2)-fx;      q=(*bx-*cx)*(*fb-*fa); 
        u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     p2[thetai]=x[thetai]-delti[thetai]/k;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     k3=func(p2)-fx;      if ((*bx-u)*(u-*cx) > 0.0) { 
          fu=(*func)(u); 
     p2[thetai]=x[thetai]-delti[thetai]/k;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        fu=(*func)(u); 
     k4=func(p2)-fx;        if (fu < *fc) { 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 #ifdef DEBUG            SHFT(*fb,*fc,fu,(*func)(u)) 
     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);            } 
 #endif      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   }        u=ulim; 
   return res;        fu=(*func)(u); 
 }      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
 /************** Inverse of matrix **************/        fu=(*func)(u); 
 void ludcmp(double **a, int n, int *indx, double *d)      } 
 {      SHFT(*ax,*bx,*cx,u) 
   int i,imax,j,k;        SHFT(*fa,*fb,*fc,fu) 
   double big,dum,sum,temp;        } 
   double *vv;  } 
    
   vv=vector(1,n);  /*************** linmin ************************/
   *d=1.0;  
   for (i=1;i<=n;i++) {  int ncom; 
     big=0.0;  double *pcom,*xicom;
     for (j=1;j<=n;j++)  double (*nrfunc)(double []); 
       if ((temp=fabs(a[i][j])) > big) big=temp;   
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     vv[i]=1.0/big;  { 
   }    double brent(double ax, double bx, double cx, 
   for (j=1;j<=n;j++) {                 double (*f)(double), double tol, double *xmin); 
     for (i=1;i<j;i++) {    double f1dim(double x); 
       sum=a[i][j];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];                double *fc, double (*func)(double)); 
       a[i][j]=sum;    int j; 
     }    double xx,xmin,bx,ax; 
     big=0.0;    double fx,fb,fa;
     for (i=j;i<=n;i++) {   
       sum=a[i][j];    ncom=n; 
       for (k=1;k<j;k++)    pcom=vector(1,n); 
         sum -= a[i][k]*a[k][j];    xicom=vector(1,n); 
       a[i][j]=sum;    nrfunc=func; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {    for (j=1;j<=n;j++) { 
         big=dum;      pcom[j]=p[j]; 
         imax=i;      xicom[j]=xi[j]; 
       }    } 
     }    ax=0.0; 
     if (j != imax) {    xx=1.0; 
       for (k=1;k<=n;k++) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         dum=a[imax][k];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         a[imax][k]=a[j][k];  #ifdef DEBUG
         a[j][k]=dum;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       *d = -(*d);  #endif
       vv[imax]=vv[j];    for (j=1;j<=n;j++) { 
     }      xi[j] *= xmin; 
     indx[j]=imax;      p[j] += xi[j]; 
     if (a[j][j] == 0.0) a[j][j]=TINY;    } 
     if (j != n) {    free_vector(xicom,1,n); 
       dum=1.0/(a[j][j]);    free_vector(pcom,1,n); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  } 
     }  
   }  char *asc_diff_time(long time_sec, char ascdiff[])
   free_vector(vv,1,n);  /* Doesn't work */  {
 ;    long sec_left, days, hours, minutes;
 }    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
 void lubksb(double **a, int n, int *indx, double b[])    hours = (sec_left) / (60*60) ;
 {    sec_left = (sec_left) %(60*60);
   int i,ii=0,ip,j;    minutes = (sec_left) /60;
   double sum;    sec_left = (sec_left) % (60);
      sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   for (i=1;i<=n;i++) {    return ascdiff;
     ip=indx[i];  }
     sum=b[ip];  
     b[ip]=b[i];  /*************** powell ************************/
     if (ii)  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];              double (*func)(double [])) 
     else if (sum) ii=i;  { 
     b[i]=sum;    void linmin(double p[], double xi[], int n, double *fret, 
   }                double (*func)(double [])); 
   for (i=n;i>=1;i--) {    int i,ibig,j; 
     sum=b[i];    double del,t,*pt,*ptt,*xit;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    double fp,fptt;
     b[i]=sum/a[i][i];    double *xits;
   }    int niterf, itmp;
 }  
     pt=vector(1,n); 
 /************ Frequencies ********************/    ptt=vector(1,n); 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    xit=vector(1,n); 
 {  /* Some frequencies */    xits=vector(1,n); 
      *fret=(*func)(p); 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double ***freq; /* Frequencies */    for (*iter=1;;++(*iter)) { 
   double *pp;      fp=(*fret); 
   double pos, k2, dateintsum=0,k2cpt=0;      ibig=0; 
   FILE *ficresp;      del=0.0; 
   char fileresp[FILENAMELENGTH];      last_time=curr_time;
        (void) gettimeofday(&curr_time,&tzp);
   pp=vector(1,nlstate);      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);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      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);
   strcpy(fileresp,"p");  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   strcat(fileresp,fileres);     for (i=1;i<=n;i++) {
   if((ficresp=fopen(fileresp,"w"))==NULL) {        printf(" %d %.12f",i, p[i]);
     printf("Problem with prevalence resultfile: %s\n", fileresp);        fprintf(ficlog," %d %.12lf",i, p[i]);
     exit(0);        fprintf(ficrespow," %.12lf", p[i]);
   }      }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      printf("\n");
   j1=0;      fprintf(ficlog,"\n");
        fprintf(ficrespow,"\n");fflush(ficrespow);
   j=cptcoveff;      if(*iter <=3){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        tm = *localtime(&curr_time.tv_sec);
          strcpy(strcurr,asctime(&tm));
   for(k1=1; k1<=j;k1++){  /*       asctime_r(&tm,strcurr); */
     for(i1=1; i1<=ncodemax[k1];i1++){        forecast_time=curr_time; 
       j1++;        itmp = strlen(strcurr);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         scanf("%d", i);*/          strcurr[itmp-1]='\0';
       for (i=-1; i<=nlstate+ndeath; i++)          printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for (jk=-1; jk<=nlstate+ndeath; jk++)          fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
           for(m=agemin; m <= agemax+3; m++)        for(niterf=10;niterf<=30;niterf+=10){
             freq[i][jk][m]=0;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                tmf = *localtime(&forecast_time.tv_sec);
       dateintsum=0;  /*      asctime_r(&tmf,strfor); */
       k2cpt=0;          strcpy(strfor,asctime(&tmf));
       for (i=1; i<=imx; i++) {          itmp = strlen(strfor);
         bool=1;          if(strfor[itmp-1]=='\n')
         if  (cptcovn>0) {          strfor[itmp-1]='\0';
           for (z1=1; z1<=cptcoveff; z1++)          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          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);
               bool=0;        }
         }      }
         if (bool==1) {      for (i=1;i<=n;i++) { 
           for(m=firstpass; m<=lastpass; m++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
             k2=anint[m][i]+(mint[m][i]/12.);        fptt=(*fret); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  #ifdef DEBUG
               if(agev[m][i]==0) agev[m][i]=agemax+1;        printf("fret=%lf \n",*fret);
               if(agev[m][i]==1) agev[m][i]=agemax+2;        fprintf(ficlog,"fret=%lf \n",*fret);
               if (m<lastpass) {  #endif
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        printf("%d",i);fflush(stdout);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        fprintf(ficlog,"%d",i);fflush(ficlog);
               }        linmin(p,xit,n,fret,func); 
                      if (fabs(fptt-(*fret)) > del) { 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          del=fabs(fptt-(*fret)); 
                 dateintsum=dateintsum+k2;          ibig=i; 
                 k2cpt++;        } 
               }  #ifdef DEBUG
             }        printf("%d %.12e",i,(*fret));
           }        fprintf(ficlog,"%d %.12e",i,(*fret));
         }        for (j=1;j<=n;j++) {
       }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                  printf(" x(%d)=%.12e",j,xit[j]);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
       if  (cptcovn>0) {        for(j=1;j<=n;j++) {
         fprintf(ficresp, "\n#********** Variable ");          printf(" p=%.12e",p[j]);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          fprintf(ficlog," p=%.12e",p[j]);
         fprintf(ficresp, "**********\n#");        }
       }        printf("\n");
       for(i=1; i<=nlstate;i++)        fprintf(ficlog,"\n");
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  #endif
       fprintf(ficresp, "\n");      } 
            if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){  #ifdef DEBUG
         if(i==(int)agemax+3)        int k[2],l;
           printf("Total");        k[0]=1;
         else        k[1]=-1;
           printf("Age %d", i);        printf("Max: %.12e",(*func)(p));
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for (j=1;j<=n;j++) {
             pp[jk] += freq[jk][m][i];          printf(" %.12e",p[j]);
         }          fprintf(ficlog," %.12e",p[j]);
         for(jk=1; jk <=nlstate ; jk++){        }
           for(m=-1, pos=0; m <=0 ; m++)        printf("\n");
             pos += freq[jk][m][i];        fprintf(ficlog,"\n");
           if(pp[jk]>=1.e-10)        for(l=0;l<=1;l++) {
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          for (j=1;j<=n;j++) {
           else            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
         for(jk=1; jk <=nlstate ; jk++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
             pp[jk] += freq[jk][m][i];        }
         }  #endif
   
         for(jk=1,pos=0; jk <=nlstate ; jk++)  
           pos += pp[jk];        free_vector(xit,1,n); 
         for(jk=1; jk <=nlstate ; jk++){        free_vector(xits,1,n); 
           if(pos>=1.e-5)        free_vector(ptt,1,n); 
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        free_vector(pt,1,n); 
           else        return; 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      } 
           if( i <= (int) agemax){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
             if(pos>=1.e-5){      for (j=1;j<=n;j++) { 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        ptt[j]=2.0*p[j]-pt[j]; 
               probs[i][jk][j1]= pp[jk]/pos;        xit[j]=p[j]-pt[j]; 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        pt[j]=p[j]; 
             }      } 
             else      fptt=(*func)(ptt); 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      if (fptt < fp) { 
           }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         }        if (t < 0.0) { 
                  linmin(p,xit,n,fret,func); 
         for(jk=-1; jk <=nlstate+ndeath; jk++)          for (j=1;j<=n;j++) { 
           for(m=-1; m <=nlstate+ndeath; m++)            xi[j][ibig]=xi[j][n]; 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            xi[j][n]=xit[j]; 
         if(i <= (int) agemax)          }
           fprintf(ficresp,"\n");  #ifdef DEBUG
         printf("\n");          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(j=1;j<=n;j++){
   }            printf(" %.12e",xit[j]);
   dateintmean=dateintsum/k2cpt;            fprintf(ficlog," %.12e",xit[j]);
            }
   fclose(ficresp);          printf("\n");
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          fprintf(ficlog,"\n");
   free_vector(pp,1,nlstate);  #endif
          }
   /* End of Freq */      } 
 }    } 
   } 
 /************ Prevalence ********************/  
 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)  /**** Prevalence limit (stable or period prevalence)  ****************/
 {  /* Some frequencies */  
    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  {
   double ***freq; /* Frequencies */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   double *pp;       matrix by transitions matrix until convergence is reached */
   double pos, k2;  
     int i, ii,j,k;
   pp=vector(1,nlstate);    double min, max, maxmin, maxmax,sumnew=0.;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* double **matprod2(); */ /* test */
      double **out, cov[NCOVMAX+1], **pmij();
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double **newm;
   j1=0;    double agefin, delaymax=50 ; /* Max number of years to converge */
    
   j=cptcoveff;    for (ii=1;ii<=nlstate+ndeath;ii++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for (j=1;j<=nlstate+ndeath;j++){
          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  for(k1=1; k1<=j;k1++){      }
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;     cov[1]=1.;
     
       for (i=-1; i<=nlstate+ndeath; i++)     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
           for(m=agemin; m <= agemax+3; m++)      newm=savm;
             freq[i][jk][m]=0;      /* Covariates have to be included here again */
            cov[2]=agefin;
       for (i=1; i<=imx; i++) {      
         bool=1;      for (k=1; k<=cptcovn;k++) {
         if  (cptcovn>0) {        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           for (z1=1; z1<=cptcoveff; z1++)        /*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]]);*/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      }
               bool=0;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         }      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
         if (bool==1) {      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
           for(m=firstpass; m<=lastpass; m++){      
             k2=anint[m][i]+(mint[m][i]/12.);      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
               if(agev[m][i]==0) agev[m][i]=agemax+1;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
               if(agev[m][i]==1) agev[m][i]=agemax+2;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
               if (m<lastpass)      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
               else      
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      savm=oldm;
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      oldm=newm;
             }      maxmax=0.;
           }      for(j=1;j<=nlstate;j++){
         }        min=1.;
       }        max=0.;
         for(i=(int)agemin; i <= (int)agemax+3; i++){        for(i=1; i<=nlstate; i++) {
           for(jk=1; jk <=nlstate ; jk++){          sumnew=0;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
               pp[jk] += freq[jk][m][i];          prlim[i][j]= newm[i][j]/(1-sumnew);
           }          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           for(jk=1; jk <=nlstate ; jk++){          max=FMAX(max,prlim[i][j]);
             for(m=-1, pos=0; m <=0 ; m++)          min=FMIN(min,prlim[i][j]);
             pos += freq[jk][m][i];        }
         }        maxmin=max-min;
                maxmax=FMAX(maxmax,maxmin);
          for(jk=1; jk <=nlstate ; jk++){      }
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      if(maxmax < ftolpl){
              pp[jk] += freq[jk][m][i];        return prlim;
          }      }
              }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  }
   
          for(jk=1; jk <=nlstate ; jk++){            /*************** transition probabilities ***************/ 
            if( i <= (int) agemax){  
              if(pos>=1.e-5){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
                probs[i][jk][j1]= pp[jk]/pos;  {
              }    /* 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
          }       model to the ncovmodel covariates (including constant and age).
                 lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         }       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     }       ncth covariate in the global vector x is given by the formula:
   }       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   free_vector(pp,1,nlstate);       Outputs ps[i][j] the probability to be observed in j being in j according to
         the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
 }  /* End of Freq */    */
     double s1, lnpijopii;
 /************* Waves Concatenation ***************/    /*double t34;*/
     int i,j,j1, nc, ii, jj;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {      for(i=1; i<= nlstate; i++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for(j=1; j<i;j++){
      Death is a valid wave (if date is known).          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            /*lnpijopii += param[i][j][nc]*cov[nc];*/
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
      and mw[mi+1][i]. dh depends on stepm.  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
      */          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   int i, mi, m;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        }
      double sum=0., jmean=0.;*/        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   int j, k=0,jk, ju, jl;            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   double sum=0.;            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   jmin=1e+5;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   jmax=-1;          }
   jmean=0.;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   for(i=1; i<=imx; i++){        }
     mi=0;      }
     m=firstpass;      
     while(s[m][i] <= nlstate){      for(i=1; i<= nlstate; i++){
       if(s[m][i]>=1)        s1=0;
         mw[++mi][i]=m;        for(j=1; j<i; j++){
       if(m >=lastpass)          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         break;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       else        }
         m++;        for(j=i+1; j<=nlstate+ndeath; j++){
     }/* end while */          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     if (s[m][i] > nlstate){          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       mi++;     /* Death is another wave */        }
       /* if(mi==0)  never been interviewed correctly before death */        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
          /* Only death is a correct wave */        ps[i][i]=1./(s1+1.);
       mw[mi][i]=m;        /* Computing other pijs */
     }        for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
     wav[i]=mi;        for(j=i+1; j<=nlstate+ndeath; j++)
     if(mi==0)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   }      } /* end i */
       
   for(i=1; i<=imx; i++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for(mi=1; mi<wav[i];mi++){        for(jj=1; jj<= nlstate+ndeath; jj++){
       if (stepm <=0)          ps[ii][jj]=0;
         dh[mi][i]=1;          ps[ii][ii]=1;
       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);      
           if(j==0) j=1;  /* Survives at least one month after exam */      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
           k=k+1;      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           if (j >= jmax) jmax=j;      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
           if (j <= jmin) jmin=j;      /*   } */
           sum=sum+j;      /*   printf("\n "); */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      /* } */
           }      /* printf("\n ");printf("%lf ",cov[2]);*/
         }      /*
         else{        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        goto end;*/
           k=k+1;      return ps;
           if (j >= jmax) jmax=j;  }
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  /**************** Product of 2 matrices ******************/
           sum=sum+j;  
         }  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
         jk= j/stepm;  {
         jl= j -jk*stepm;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         ju= j -(jk+1)*stepm;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         if(jl <= -ju)    /* in, b, out are matrice of pointers which should have been initialized 
           dh[mi][i]=jk;       before: only the contents of out is modified. The function returns
         else       a pointer to pointers identical to out */
           dh[mi][i]=jk+1;    int i, j, k;
         if(dh[mi][i]==0)    for(i=nrl; i<= nrh; i++)
           dh[mi][i]=1; /* At least one step */      for(k=ncolol; k<=ncoloh; k++){
       }        out[i][k]=0.;
     }        for(j=ncl; j<=nch; j++)
   }          out[i][k] +=in[i][j]*b[j][k];
   jmean=sum/k;      }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    return out;
  }  }
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)  
 {  /************* Higher Matrix Product ***************/
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   cptcoveff=0;  {
      /* Computes the transition matrix starting at age 'age' over 
   for (k=0; k<19; k++) Ndum[k]=0;       'nhstepm*hstepm*stepm' months (i.e. until
   for (k=1; k<=7; k++) ncodemax[k]=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     for (i=1; i<=imx; i++) {       (typically every 2 years instead of every month which is too big 
       ij=(int)(covar[Tvar[j]][i]);       for the memory).
       Ndum[ij]++;       Model is determined by parameters x and covariates have to be 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/       included manually here. 
       if (ij > cptcode) cptcode=ij;  
     }       */
   
     for (i=0; i<=cptcode; i++) {    int i, j, d, h, k;
       if(Ndum[i]!=0) ncodemax[j]++;    double **out, cov[NCOVMAX+1];
     }    double **newm;
     ij=1;  
     /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
     for (i=1; i<=ncodemax[j]; i++) {      for (j=1;j<=nlstate+ndeath;j++){
       for (k=0; k<=19; k++) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
         if (Ndum[k] != 0) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
           nbcode[Tvar[j]][ij]=k;      }
              /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           ij++;    for(h=1; h <=nhstepm; h++){
         }      for(d=1; d <=hstepm; d++){
         if (ij > ncodemax[j]) break;        newm=savm;
       }          /* Covariates have to be included here again */
     }        cov[1]=1.;
   }          cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) 
  for (k=0; k<19; k++) Ndum[k]=0;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
  for (i=1; i<=ncovmodel-2; i++) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       ij=Tvar[i];        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
       Ndum[ij]++;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     }  
   
  ij=1;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
  for (i=1; i<=10; i++) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
      Tvaraff[ij]=i;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
      ij++;        savm=oldm;
    }        oldm=newm;
  }      }
        for(i=1; i<=nlstate+ndeath; i++)
     cptcoveff=ij-1;        for(j=1;j<=nlstate+ndeath;j++) {
 }          po[i][j][h]=newm[i][j];
           /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
 /*********** Health Expectancies ****************/        }
       /*printf("h=%d ",h);*/
 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 )    } /* end h */
   /*     printf("\n H=%d \n",h); */
 {    return po;
   /* Health expectancies */  }
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  
   double age, agelim, hf;  
   double ***p3mat,***varhe;  /*************** log-likelihood *************/
   double **dnewm,**doldm;  double func( double *x)
   double *xp;  {
   double **gp, **gm;    int i, ii, j, k, mi, d, kk;
   double ***gradg, ***trgradg;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   int theta;    double **out;
     double sw; /* Sum of weights */
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    double lli; /* Individual log likelihood */
   xp=vector(1,npar);    int s1, s2;
   dnewm=matrix(1,nlstate*2,1,npar);    double bbh, survp;
   doldm=matrix(1,nlstate*2,1,nlstate*2);    long ipmx;
      /*extern weight */
   fprintf(ficreseij,"# Health expectancies\n");    /* We are differentiating ll according to initial status */
   fprintf(ficreseij,"# Age");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for(i=1; i<=nlstate;i++)    /*for(i=1;i<imx;i++) 
     for(j=1; j<=nlstate;j++)      printf(" %d\n",s[4][i]);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    */
   fprintf(ficreseij,"\n");    cov[1]=1.;
   
   if(estepm < stepm){    for(k=1; k<=nlstate; k++) ll[k]=0.;
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }    if(mle==1){
   else  hstepm=estepm;        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* We compute the life expectancy from trapezoids spaced every estepm months        /* Computes the values of the ncovmodel covariates of the model
    * This is mainly to measure the difference between two models: for example           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
    * if stepm=24 months pijx are given only every 2 years and by summing them           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
    * we are calculating an estimate of the Life Expectancy assuming a linear           to be observed in j being in i according to the model.
    * progression inbetween and thus overestimating or underestimating according         */
    * to the curvature of the survival function. If, for the same date, we        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months          cov[2+k]=covar[Tvar[k]][i];
    * to compare the new estimate of Life expectancy with the same linear        }
    * hypothesis. A more precise result, taking into account a more precise        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
    * curvature will be obtained if estepm is as small as stepm. */           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
            has been calculated etc */
   /* For example we decided to compute the life expectancy with the smallest unit */        for(mi=1; mi<= wav[i]-1; mi++){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          for (ii=1;ii<=nlstate+ndeath;ii++)
      nhstepm is the number of hstepm from age to agelim            for (j=1;j<=nlstate+ndeath;j++){
      nstepm is the number of stepm from age to agelin.              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      Look at hpijx to understand the reason of that which relies in memory size              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      and note for a fixed period like estepm months */            }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for(d=0; d<dh[mi][i]; d++){
      survival function given by stepm (the optimization length). Unfortunately it            newm=savm;
      means that if the survival funtion is printed only each two years of age and if            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            for (kk=1; kk<=cptcovage;kk++) {
      results. So we changed our mind and took the option of the best precision.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
   */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   agelim=AGESUP;            savm=oldm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            oldm=newm;
     /* nhstepm age range expressed in number of stepm */          } /* end mult */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     /* if (stepm >= YEARM) hstepm=1;*/          /* But now since version 0.9 we anticipate for bias at large stepm.
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           * (in months) between two waves is not a multiple of stepm, we rounded to 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);           * the nearest (and in case of equal distance, to the lowest) interval but now
     gp=matrix(0,nhstepm,1,nlstate*2);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     gm=matrix(0,nhstepm,1,nlstate*2);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
     /* Computed by stepm unit matrices, product of hstepm matrices, stored           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */           * -stepm/2 to stepm/2 .
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);             * For stepm=1 the results are the same as for previous versions of Imach.
             * For stepm > 1 the results are less biased than in previous versions. 
            */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     /* Computing Variances of health expectancies */          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
      for(theta=1; theta <=npar; theta++){           * is higher than the multiple of stepm and negative otherwise.
       for(i=1; i<=npar; i++){           */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       }          if( s2 > nlstate){ 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              /* i.e. if s2 is a death state and if the date of death is known 
                 then the contribution to the likelihood is the probability to 
       cptj=0;               die between last step unit time and current  step unit time, 
       for(j=1; j<= nlstate; j++){               which is also equal to probability to die before dh 
         for(i=1; i<=nlstate; i++){               minus probability to die before dh-stepm . 
           cptj=cptj+1;               In version up to 0.92 likelihood was computed
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          as if date of death was unknown. Death was treated as any other
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          health state: the date of the interview describes the actual state
           }          and not the date of a change in health state. The former idea was
         }          to consider that at each interview the state was recorded
       }          (healthy, disable or death) and IMaCh was corrected; but when we
                introduced the exact date of death then we should have modified
                the contribution of an exact death to the likelihood. This new
       for(i=1; i<=npar; i++)          contribution is smaller and very dependent of the step unit
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          stepm. It is no more the probability to die between last interview
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            and month of death but the probability to survive from last
                interview up to one month before death multiplied by the
       cptj=0;          probability to die within a month. Thanks to Chris
       for(j=1; j<= nlstate; j++){          Jackson for correcting this bug.  Former versions increased
         for(i=1;i<=nlstate;i++){          mortality artificially. The bad side is that we add another loop
           cptj=cptj+1;          which slows down the processing. The difference can be up to 10%
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          lower mortality.
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            */
           }            lli=log(out[s1][s2] - savm[s1][s2]);
         }  
       }  
                } else if  (s2==-2) {
                for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(j=1; j<= nlstate*2; j++)            /*survp += out[s1][j]; */
         for(h=0; h<=nhstepm-1; h++){            lli= log(survp);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          }
         }          
           else if  (s2==-4) { 
      }            for (j=3,survp=0. ; j<=nlstate; j++)  
                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 /* End theta */            lli= log(survp); 
           } 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  
           else if  (s2==-5) { 
      for(h=0; h<=nhstepm-1; h++)            for (j=1,survp=0. ; j<=2; j++)  
       for(j=1; j<=nlstate*2;j++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         for(theta=1; theta <=npar; theta++)            lli= log(survp); 
         trgradg[h][j][theta]=gradg[h][theta][j];          } 
           
           else{
      for(i=1;i<=nlstate*2;i++)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(j=1;j<=nlstate*2;j++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         varhe[i][j][(int)age] =0.;          } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     for(h=0;h<=nhstepm-1;h++){          /*if(lli ==000.0)*/
       for(k=0;k<=nhstepm-1;k++){          /*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); */
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          ipmx +=1;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          sw += weight[i];
         for(i=1;i<=nlstate*2;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(j=1;j<=nlstate*2;j++)        } /* end of wave */
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;      } /* end of individual */
       }    }  else if(mle==2){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
     /* Computing expectancies */          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
       for(j=1; j<=nlstate;j++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            }
                    for(d=0; d<=dh[mi][i]; d++){
 /* 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]);*/            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficreseij,"%3.0f",age );            }
     cptj=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i=1; i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<=nlstate;j++){            savm=oldm;
         cptj++;            oldm=newm;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          } /* end mult */
       }        
     fprintf(ficreseij,"\n");          s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
     free_matrix(gm,0,nhstepm,1,nlstate*2);          bbh=(double)bh[mi][i]/(double)stepm; 
     free_matrix(gp,0,nhstepm,1,nlstate*2);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     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==3){  /* exponential inter-extrapolation */
   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,"# Covariances of life expectancies\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]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       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==4){  /* ml=4 no 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          
      results. So we changed our mind and took the option of the best precision.            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            savm=oldm;
   agelim = AGESUP;            oldm=newm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          } /* end mult */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          s1=s[mw[mi][i]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s2=s[mw[mi+1][i]][i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          if( s2 > nlstate){ 
     gp=matrix(0,nhstepm,1,nlstate);            lli=log(out[s1][s2] - savm[s1][s2]);
     gm=matrix(0,nhstepm,1,nlstate);          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(theta=1; theta <=npar; theta++){          }
       for(i=1; i<=npar; i++){ /* Computes gradient */          ipmx +=1;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* end of wave */
       } /* end of individual */
       if (popbased==1) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         for(i=1; i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           prlim[i][i]=probs[(int)age][i][ij];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<= nlstate; j++){            for (j=1;j<=nlstate+ndeath;j++){
         for(h=0; h<=nhstepm; h++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            }
         }          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
                cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1; i<=npar; i++) /* Computes gradient */            for (kk=1; kk<=cptcovage;kk++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if (popbased==1) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(i=1; i<=nlstate;i++)            savm=oldm;
           prlim[i][i]=probs[(int)age][i][ij];            oldm=newm;
       }          } /* end mult */
         
       for(j=1; j<= nlstate; j++){          s1=s[mw[mi][i]][i];
         for(h=0; h<=nhstepm; h++){          s2=s[mw[mi+1][i]][i];
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          ipmx +=1;
         }          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]);*/
       for(j=1; j<= nlstate; j++)        } /* end of wave */
         for(h=0; h<=nhstepm; h++){      } /* end of individual */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     } /* End theta */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    return -l;
   }
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)  /*************** log-likelihood *************/
         for(theta=1; theta <=npar; theta++)  double funcone( double *x)
           trgradg[h][j][theta]=gradg[h][theta][j];  {
     /* Same as likeli but slower because of a lot of printf and if */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    int i, ii, j, k, mi, d, kk;
     for(i=1;i<=nlstate;i++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       for(j=1;j<=nlstate;j++)    double **out;
         vareij[i][j][(int)age] =0.;    double lli; /* Individual log likelihood */
     double llt;
     for(h=0;h<=nhstepm;h++){    int s1, s2;
       for(k=0;k<=nhstepm;k++){    double bbh, survp;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    /*extern weight */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    /* We are differentiating ll according to initial status */
         for(i=1;i<=nlstate;i++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           for(j=1;j<=nlstate;j++)    /*for(i=1;i<imx;i++) 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      printf(" %d\n",s[4][i]);
       }    */
     }    cov[1]=1.;
   
     fprintf(ficresvij,"%.0f ",age );    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }      for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficresvij,"\n");        for (ii=1;ii<=nlstate+ndeath;ii++)
     free_matrix(gp,0,nhstepm,1,nlstate);          for (j=1;j<=nlstate+ndeath;j++){
     free_matrix(gm,0,nhstepm,1,nlstate);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(d=0; d<dh[mi][i]; d++){
   } /* End age */          newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_vector(xp,1,npar);          for (kk=1; kk<=cptcovage;kk++) {
   free_matrix(doldm,1,nlstate,1,npar);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_matrix(dnewm,1,nlstate,1,nlstate);          }
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /************ Variance of prevlim ******************/          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
 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)          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
 {          savm=oldm;
   /* Variance of prevalence limit */          oldm=newm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        } /* end mult */
   double **newm;        
   double **dnewm,**doldm;        s1=s[mw[mi][i]][i];
   int i, j, nhstepm, hstepm;        s2=s[mw[mi+1][i]][i];
   int k, cptcode;        bbh=(double)bh[mi][i]/(double)stepm; 
   double *xp;        /* bias is positive if real duration
   double *gp, *gm;         * is higher than the multiple of stepm and negative otherwise.
   double **gradg, **trgradg;         */
   double age,agelim;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   int theta;          lli=log(out[s1][s2] - savm[s1][s2]);
            } else if  (s2==-2) {
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          for (j=1,survp=0. ; j<=nlstate; j++) 
   fprintf(ficresvpl,"# Age");            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   for(i=1; i<=nlstate;i++)          lli= log(survp);
       fprintf(ficresvpl," %1d-%1d",i,i);        }else if (mle==1){
   fprintf(ficresvpl,"\n");          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
   xp=vector(1,npar);          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 */
   dnewm=matrix(1,nlstate,1,npar);        } else if(mle==3){  /* exponential inter-extrapolation */
   doldm=matrix(1,nlstate,1,nlstate);          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
          } else if (mle==4){  /* mle=4 no inter-extrapolation */
   hstepm=1*YEARM; /* Every year of age */          lli=log(out[s1][s2]); /* Original formula */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } else{  /* mle=0 back to 1 */
   agelim = AGESUP;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          /*lli=log(out[s1][s2]); */ /* Original formula */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } /* End of if */
     if (stepm >= YEARM) hstepm=1;        ipmx +=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        sw += weight[i];
     gradg=matrix(1,npar,1,nlstate);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gp=vector(1,nlstate);        /*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]); */
     gm=vector(1,nlstate);        if(globpr){
           fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     for(theta=1; theta <=npar; theta++){   %11.6f %11.6f %11.6f ", \
       for(i=1; i<=npar; i++){ /* Computes gradient */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            llt +=ll[k]*gipmx/gsw;
       for(i=1;i<=nlstate;i++)            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         gp[i] = prlim[i][i];          }
              fprintf(ficresilk," %10.6f\n", -llt);
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      } /* end of wave */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } /* end of individual */
       for(i=1;i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         gm[i] = prlim[i][i];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for(i=1;i<=nlstate;i++)    if(globpr==0){ /* First time we count the contributions and weights */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      gipmx=ipmx;
     } /* End theta */      gsw=sw;
     }
     trgradg =matrix(1,nlstate,1,npar);    return -l;
   }
     for(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     for(i=1;i<=nlstate;i++)  {
       varpl[i][(int)age] =0.;    /* This routine should help understanding what is done with 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);       the selection of individuals/waves and
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);       to check the exact contribution to the likelihood.
     for(i=1;i<=nlstate;i++)       Plotting could be done.
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */     */
     int k;
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    if(*globpri !=0){ /* Just counts and sums, no printings */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      strcpy(fileresilk,"ilk"); 
     fprintf(ficresvpl,"\n");      strcat(fileresilk,fileres);
     free_vector(gp,1,nlstate);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     free_vector(gm,1,nlstate);        printf("Problem with resultfile: %s\n", fileresilk);
     free_matrix(gradg,1,npar,1,nlstate);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     free_matrix(trgradg,1,nlstate,1,npar);      }
   } /* End age */      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   free_vector(xp,1,npar);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   free_matrix(doldm,1,nlstate,1,npar);      for(k=1; k<=nlstate; k++) 
   free_matrix(dnewm,1,nlstate,1,nlstate);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 }    }
   
 /************ Variance of one-step probabilities  ******************/    *fretone=(*funcone)(p);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    if(*globpri !=0){
 {      fclose(ficresilk);
   int i, j, i1, k1, j1, z1;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   int k=0, cptcode;      fflush(fichtm); 
   double **dnewm,**doldm;    } 
   double *xp;    return;
   double *gp, *gm;  }
   double **gradg, **trgradg;  
   double age,agelim, cov[NCOVMAX];  
   int theta;  /*********** Maximum Likelihood Estimation ***************/
   char fileresprob[FILENAMELENGTH];  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   strcpy(fileresprob,"prob");  {
   strcat(fileresprob,fileres);    int i,j, iter;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    double **xi;
     printf("Problem with resultfile: %s\n", fileresprob);    double fret;
   }    double fretone; /* Only one call to likelihood */
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    /*  char filerespow[FILENAMELENGTH];*/
      xi=matrix(1,npar,1,npar);
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    for (i=1;i<=npar;i++)
   fprintf(ficresprob,"# Age");      for (j=1;j<=npar;j++)
   for(i=1; i<=nlstate;i++)        xi[i][j]=(i==j ? 1.0 : 0.0);
     for(j=1; j<=(nlstate+ndeath);j++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
   fprintf(ficresprob,"\n");      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
   xp=vector(1,npar);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=nlstate;i++)
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      for(j=1;j<=nlstate+ndeath;j++)
          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   cov[1]=1;    fprintf(ficrespow,"\n");
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    powell(p,xi,npar,ftol,&iter,&fret,func);
   j1=0;  
   for(k1=1; k1<=1;k1++){    free_matrix(xi,1,npar,1,npar);
     for(i1=1; i1<=ncodemax[k1];i1++){    fclose(ficrespow);
     j1++;    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));
     if  (cptcovn>0) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fprintf(ficresprob, "\n#********** Variable ");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  }
       fprintf(ficresprob, "**********\n#");  
     }  /**** Computes Hessian and covariance matrix ***/
      void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for (age=bage; age<=fage; age ++){  {
         cov[2]=age;    double  **a,**y,*x,pd;
         for (k=1; k<=cptcovn;k++) {    double **hess;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    int i, j,jk;
              int *indx;
         }  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         for (k=1; k<=cptcovprod;k++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    void lubksb(double **a, int npar, int *indx, double b[]) ;
            void ludcmp(double **a, int npar, int *indx, double *d) ;
         gradg=matrix(1,npar,1,9);    double gompertz(double p[]);
         trgradg=matrix(1,9,1,npar);    hess=matrix(1,npar,1,npar);
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    printf("\nCalculation of the hessian matrix. Wait...\n");
        fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         for(theta=1; theta <=npar; theta++){    for (i=1;i<=npar;i++){
           for(i=1; i<=npar; i++)      printf("%d",i);fflush(stdout);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      fprintf(ficlog,"%d",i);fflush(ficlog);
               
           pmij(pmmij,cov,ncovmodel,xp,nlstate);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
                
           k=0;      /*  printf(" %f ",p[i]);
           for(i=1; i<= (nlstate+ndeath); i++){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
             for(j=1; j<=(nlstate+ndeath);j++){    }
               k=k+1;    
               gp[k]=pmmij[i][j];    for (i=1;i<=npar;i++) {
             }      for (j=1;j<=npar;j++)  {
           }        if (j>i) { 
                    printf(".%d%d",i,j);fflush(stdout);
           for(i=1; i<=npar; i++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          hess[i][j]=hessij(p,delti,i,j,func,npar);
              
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          hess[j][i]=hess[i][j];    
           k=0;          /*printf(" %lf ",hess[i][j]);*/
           for(i=1; i<=(nlstate+ndeath); i++){        }
             for(j=1; j<=(nlstate+ndeath);j++){      }
               k=k+1;    }
               gm[k]=pmmij[i][j];    printf("\n");
             }    fprintf(ficlog,"\n");
           }  
          printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      
         }    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    x=vector(1,npar);
           for(theta=1; theta <=npar; theta++)    indx=ivector(1,npar);
             trgradg[j][theta]=gradg[theta][j];    for (i=1;i<=npar;i++)
              for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    ludcmp(a,npar,indx,&pd);
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  
            for (j=1;j<=npar;j++) {
         pmij(pmmij,cov,ncovmodel,x,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
              x[j]=1;
         k=0;      lubksb(a,npar,indx,x);
         for(i=1; i<=(nlstate+ndeath); i++){      for (i=1;i<=npar;i++){ 
           for(j=1; j<=(nlstate+ndeath);j++){        matcov[i][j]=x[i];
             k=k+1;      }
             gm[k]=pmmij[i][j];    }
           }  
         }    printf("\n#Hessian matrix#\n");
          fprintf(ficlog,"\n#Hessian matrix#\n");
      /*printf("\n%d ",(int)age);    for (i=1;i<=npar;i++) { 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      for (j=1;j<=npar;j++) { 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        printf("%.3e ",hess[i][j]);
      }*/        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
         fprintf(ficresprob,"\n%d ",(int)age);      printf("\n");
       fprintf(ficlog,"\n");
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    }
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));  
      /* Recompute Inverse */
       }    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    ludcmp(a,npar,indx,&pd);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /*  printf("\n#Hessian matrix recomputed#\n");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }    for (j=1;j<=npar;j++) {
   free_vector(xp,1,npar);      for (i=1;i<=npar;i++) x[i]=0;
   fclose(ficresprob);      x[j]=1;
        lubksb(a,npar,indx,x);
 }      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
 /******************* Printing html file ***********/        printf("%.3e ",y[i][j]);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        fprintf(ficlog,"%.3e ",y[i][j]);
  int lastpass, int stepm, int weightopt, char model[],\      }
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \      printf("\n");
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      fprintf(ficlog,"\n");
  char version[], int popforecast, int estepm ){    }
   int jj1, k1, i1, cpt;    */
   FILE *fichtm;  
   /*char optionfilehtm[FILENAMELENGTH];*/    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
   strcpy(optionfilehtm,optionfile);    free_vector(x,1,npar);
   strcat(optionfilehtm,".htm");    free_ivector(indx,1,npar);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    free_matrix(hess,1,npar,1,npar);
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }  
   }
  fprintf(fichtm,"<body> <font size=\"2\">%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  /*************** hessian matrix ****************/
 \n  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 Total number of observations=%d <br>\n  {
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    int i;
 <hr  size=\"2\" color=\"#EC5E5E\">    int l=1, lmax=20;
  <ul><li>Outputs files<br>\n    double k1,k2;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    double p2[MAXPARM+1]; /* identical to x */
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    double res;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    double fx;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    int k=0,kmax=10;
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    double l1;
   
  fprintf(fichtm,"\n    fx=func(x);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    for (i=1;i<=npar;i++) p2[i]=x[i];
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      l1=pow(10,l);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      delts=delt;
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
  if(popforecast==1) fprintf(fichtm,"\n        p2[theta]=x[theta] +delt;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        p2[theta]=x[theta]-delt;
         <br>",fileres,fileres,fileres,fileres);        k2=func(p2)-fx;
  else        /*res= (k1-2.0*fx+k2)/delt/delt; */
    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);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 fprintf(fichtm," <li>Graphs</li><p>");        
   #ifdef DEBUGHESS
  m=cptcoveff;        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);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        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);
   #endif
  jj1=0;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
  for(k1=1; k1<=m;k1++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
    for(i1=1; i1<=ncodemax[k1];i1++){          k=kmax;
        jj1++;        }
        if (cptcovn > 0) {        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          k=kmax; l=lmax*10.;
          for (cpt=1; cpt<=cptcoveff;cpt++)        }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          delts=delt;
        }        }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        }
        for(cpt=1; cpt<nlstate;cpt++){    delti[theta]=delts;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    return res; 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
        }  }
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 interval) in state (%d): v%s%d%d.gif <br>  {
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      int i;
      }    int l=1, l1, lmax=20;
      for(cpt=1; cpt<=nlstate;cpt++) {    double k1,k2,k3,k4,res,fx;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    double p2[MAXPARM+1];
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    int k;
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    fx=func(x);
 health expectancies in states (1) and (2): e%s%d.gif<br>    for (k=1; k<=2; k++) {
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      for (i=1;i<=npar;i++) p2[i]=x[i];
 fprintf(fichtm,"\n</body>");      p2[thetai]=x[thetai]+delti[thetai]/k;
    }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
    }      k1=func(p2)-fx;
 fclose(fichtm);    
 }      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 /******************* Gnuplot file **************/      k2=func(p2)-fx;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
   strcpy(optionfilegnuplot,optionfilefiname);    
   strcat(optionfilegnuplot,".gp.txt");      p2[thetai]=x[thetai]-delti[thetai]/k;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     printf("Problem with file %s",optionfilegnuplot);      k4=func(p2)-fx;
   }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
 #ifdef windows      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(ficgp,"cd \"%s\" \n",pathc);      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);
 #endif  #endif
 m=pow(2,cptcoveff);    }
      return res;
  /* 1eme*/  }
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);  { 
     int i,imax,j,k; 
 for (i=1; i<= nlstate ; i ++) {    double big,dum,sum,temp; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double *vv; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }    vv=vector(1,n); 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    *d=1.0; 
     for (i=1; i<= nlstate ; i ++) {    for (i=1;i<=n;i++) { 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      big=0.0; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for (j=1;j<=n;j++) 
 }        if ((temp=fabs(a[i][j])) > big) big=temp; 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
      for (i=1; i<= nlstate ; i ++) {      vv[i]=1.0/big; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (j=1;j<=n;j++) { 
 }        for (i=1;i<j;i++) { 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        a[i][j]=sum; 
    }      } 
   }      big=0.0; 
   /*2 eme*/      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
   for (k1=1; k1<= m ; k1 ++) {        for (k=1;k<j;k++) 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);          sum -= a[i][k]*a[k][j]; 
            a[i][j]=sum; 
     for (i=1; i<= nlstate+1 ; i ++) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       k=2*i;          big=dum; 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          imax=i; 
       for (j=1; j<= nlstate+1 ; j ++) {        } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if (j != imax) { 
 }          for (k=1;k<=n;k++) { 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          dum=a[imax][k]; 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          a[imax][k]=a[j][k]; 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          a[j][k]=dum; 
       for (j=1; j<= nlstate+1 ; j ++) {        } 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        *d = -(*d); 
         else fprintf(ficgp," \%%*lf (\%%*lf)");        vv[imax]=vv[j]; 
 }        } 
       fprintf(ficgp,"\" t\"\" w l 0,");      indx[j]=imax; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       for (j=1; j<= nlstate+1 ; j ++) {      if (j != n) { 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        dum=1.0/(a[j][j]); 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 }        } 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    } 
       else fprintf(ficgp,"\" t\"\" w l 0,");    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  } 
   }  
    void lubksb(double **a, int n, int *indx, double b[]) 
   /*3eme*/  { 
     int i,ii=0,ip,j; 
   for (k1=1; k1<= m ; k1 ++) {    double sum; 
     for (cpt=1; cpt<= nlstate ; cpt ++) {   
       k=2+nlstate*(2*cpt-2);    for (i=1;i<=n;i++) { 
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      ip=indx[i]; 
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      sum=b[ip]; 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      b[ip]=b[i]; 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      if (ii) 
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      else if (sum) ii=i; 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      b[i]=sum; 
     } 
 */    for (i=n;i>=1;i--) { 
       for (i=1; i< nlstate ; i ++) {      sum=b[i]; 
         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);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
       }    } 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  } 
     }  
     }  void pstamp(FILE *fichier)
    {
   /* CV preval stat */    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     for (k1=1; k1<= m ; k1 ++) {  }
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;  /************ Frequencies ********************/
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   {  /* Some frequencies */
       for (i=1; i< nlstate ; i ++)    
         fprintf(ficgp,"+$%d",k+i+1);    int i, m, jk, k1,i1, j1, bool, z1,j;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    int first;
          double ***freq; /* Frequencies */
       l=3+(nlstate+ndeath)*cpt;    double *pp, **prop;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       for (i=1; i< nlstate ; i ++) {    char fileresp[FILENAMELENGTH];
         l=3+(nlstate+ndeath)*cpt;    
         fprintf(ficgp,"+$%d",l+i+1);    pp=vector(1,nlstate);
       }    prop=matrix(1,nlstate,iagemin,iagemax+3);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      strcpy(fileresp,"p");
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    strcat(fileresp,fileres);
     }    if((ficresp=fopen(fileresp,"w"))==NULL) {
   }        printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   /* proba elementaires */      exit(0);
    for(i=1,jk=1; i <=nlstate; i++){    }
     for(k=1; k <=(nlstate+ndeath); k++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       if (k != i) {    j1=0;
         for(j=1; j <=ncovmodel; j++){    
            j=cptcoveff;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           jk++;  
           fprintf(ficgp,"\n");    first=1;
         }  
       }    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
     }    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
     }    /*    j1++;
   */
     for(jk=1; jk <=m; jk++) {    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
    i=1;          scanf("%d", i);*/
    for(k2=1; k2<=nlstate; k2++) {        for (i=-5; i<=nlstate+ndeath; i++)  
      k3=i;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
      for(k=1; k<=(nlstate+ndeath); k++) {            for(m=iagemin; m <= iagemax+3; m++)
        if (k != k2){              freq[i][jk][m]=0;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        
 ij=1;        for (i=1; i<=nlstate; i++)  
         for(j=3; j <=ncovmodel; j++) {          for(m=iagemin; m <= iagemax+3; m++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            prop[i][m]=0;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        
             ij++;        dateintsum=0;
           }        k2cpt=0;
           else        for (i=1; i<=imx; i++) {
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          bool=1;
         }          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           fprintf(ficgp,")/(1");            for (z1=1; z1<=cptcoveff; z1++)       
                      if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
         for(k1=1; k1 <=nlstate; k1++){                    /* Tests if the value of each of the covariates of i is equal to filter j1 */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                bool=0;
 ij=1;                /* 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(j=3; j <=ncovmodel; j++){                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
             ij++;              } 
           }          }
           else   
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          if (bool==1){
           }            for(m=firstpass; m<=lastpass; m++){
           fprintf(ficgp,")");              k2=anint[m][i]+(mint[m][i]/12.);
         }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         i=i+ncovmodel;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
        }                if (m<lastpass) {
      }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);                }
    }                
                    if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   fclose(ficgp);                  dateintsum=dateintsum+k2;
 }  /* end gnuplot */                  k2cpt++;
                 }
                 /*}*/
 /*************** Moving average **************/            }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          }
         } /* end i */
   int i, cpt, cptcod;         
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       for (i=1; i<=nlstate;i++)        pstamp(ficresp);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        if  (cptcovn>0) {
           mobaverage[(int)agedeb][i][cptcod]=0.;          fprintf(ficresp, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          fprintf(ficresp, "**********\n#");
       for (i=1; i<=nlstate;i++){          fprintf(ficlog, "\n#********** Variable "); 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for (cpt=0;cpt<=4;cpt++){          fprintf(ficlog, "**********\n#");
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        }
           }        for(i=1; i<=nlstate;i++) 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         }        fprintf(ficresp, "\n");
       }        
     }        for(i=iagemin; i <= iagemax+3; i++){
              if(i==iagemax+3){
 }            fprintf(ficlog,"Total");
           }else{
             if(first==1){
 /************** Forecasting ******************/              first=0;
 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){              printf("See log file for details...\n");
              }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            fprintf(ficlog,"Age %d", i);
   int *popage;          }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for(jk=1; jk <=nlstate ; jk++){
   double *popeffectif,*popcount;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   double ***p3mat;              pp[jk] += freq[jk][m][i]; 
   char fileresf[FILENAMELENGTH];          }
           for(jk=1; jk <=nlstate ; jk++){
  agelim=AGESUP;            for(m=-1, pos=0; m <=0 ; m++)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              if(first==1){
                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                }
   strcpy(fileresf,"f");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   strcat(fileresf,fileres);            }else{
   if((ficresf=fopen(fileresf,"w"))==NULL) {              if(first==1)
     printf("Problem with forecast resultfile: %s\n", fileresf);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   printf("Computing forecasting: result on file '%s' \n", fileresf);            }
           }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
           for(jk=1; jk <=nlstate ; jk++){
   if (mobilav==1) {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              pp[jk] += freq[jk][m][i];
     movingaverage(agedeb, fage, ageminpar, mobaverage);          }       
   }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   stepsize=(int) (stepm+YEARM-1)/YEARM;            posprop += prop[jk][i];
   if (stepm<=12) stepsize=1;          }
            for(jk=1; jk <=nlstate ; jk++){
   agelim=AGESUP;            if(pos>=1.e-5){
                if(first==1)
   hstepm=1;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   hstepm=hstepm/stepm;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   yp1=modf(dateintmean,&yp);            }else{
   anprojmean=yp;              if(first==1)
   yp2=modf((yp1*12),&yp);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   mprojmean=yp;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   yp1=modf((yp2*30.5),&yp);            }
   jprojmean=yp;            if( i <= iagemax){
   if(jprojmean==0) jprojmean=1;              if(pos>=1.e-5){
   if(mprojmean==0) jprojmean=1;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                  /*probs[i][jk][j1]= pp[jk]/pos;*/
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                }
   for(cptcov=1;cptcov<=i2;cptcov++){              else
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       k=k+1;            }
       fprintf(ficresf,"\n#******");          }
       for(j=1;j<=cptcoveff;j++) {          
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(jk=-1; jk <=nlstate+ndeath; jk++)
       }            for(m=-1; m <=nlstate+ndeath; m++)
       fprintf(ficresf,"******\n");              if(freq[jk][m][i] !=0 ) {
       fprintf(ficresf,"# StartingAge FinalAge");              if(first==1)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                      fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                    }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          if(i <= iagemax)
         fprintf(ficresf,"\n");            fprintf(ficresp,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            if(first==1)
             printf("Others in log...\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          fprintf(ficlog,"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        }
           nhstepm = nhstepm/hstepm;        /*}*/
              }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    dateintmean=dateintsum/k2cpt; 
           oldm=oldms;savm=savms;   
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fclose(ficresp);
            free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
           for (h=0; h<=nhstepm; h++){    free_vector(pp,1,nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    /* End of Freq */
             }  }
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;  /************ Prevalence ********************/
               for(i=1; i<=nlstate;i++) {                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)
                 if (mobilav==1)  {  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                 else {       in each health status at the date of interview (if between dateprev1 and dateprev2).
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       We still use firstpass and lastpass as another selection.
                 }    */
                   
               }    int i, m, jk, k1, i1, j1, bool, z1,j;
               if (h==(int)(calagedate+12*cpt)){    double ***freq; /* Frequencies */
                 fprintf(ficresf," %.3f", kk1);    double *pp, **prop;
                            double pos,posprop; 
               }    double  y2; /* in fractional years */
             }    int iagemin, iagemax;
           }    int first; /** to stop verbosity which is redirected to log file */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    iagemin= (int) agemin;
       }    iagemax= (int) agemax;
     }    /*pp=vector(1,nlstate);*/
   }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
            /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    j1=0;
     
   fclose(ficresf);    /*j=cptcoveff;*/
 }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 /************** Forecasting ******************/    
 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){    first=1;
      for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      /*for(i1=1; i1<=ncodemax[k1];i1++){
   int *popage;        j1++;*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        
   double *popeffectif,*popcount;        for (i=1; i<=nlstate; i++)  
   double ***p3mat,***tabpop,***tabpopprev;          for(m=iagemin; m <= iagemax+3; m++)
   char filerespop[FILENAMELENGTH];            prop[i][m]=0.0;
        
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (i=1; i<=imx; i++) { /* Each individual */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          bool=1;
   agelim=AGESUP;          if  (cptcovn>0) {
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                bool=0;
            } 
            if (bool==1) { 
   strcpy(filerespop,"pop");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   strcat(filerespop,fileres);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     printf("Problem with forecast resultfile: %s\n", filerespop);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   printf("Computing forecasting: result on file '%s' \n", filerespop);                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 (cptcoveff==0) ncodemax[cptcoveff]=1;                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
   if (mobilav==1) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                } 
     movingaverage(agedeb, fage, ageminpar, mobaverage);              }
   }            } /* end selection of waves */
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }
   if (stepm<=12) stepsize=1;        for(i=iagemin; i <= iagemax+3; i++){  
            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   agelim=AGESUP;            posprop += prop[jk][i]; 
            } 
   hstepm=1;          
   hstepm=hstepm/stepm;          for(jk=1; jk <=nlstate ; jk++){     
              if( i <=  iagemax){ 
   if (popforecast==1) {              if(posprop>=1.e-5){ 
     if((ficpop=fopen(popfile,"r"))==NULL) {                probs[i][jk][j1]= prop[jk][i]/posprop;
       printf("Problem with population file : %s\n",popfile);exit(0);              } else{
     }                if(first==1){
     popage=ivector(0,AGESUP);                  first=0;
     popeffectif=vector(0,AGESUP);                  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]);
     popcount=vector(0,AGESUP);                }
                  }
     i=1;              } 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          }/* end jk */ 
            }/* end i */ 
     imx=i;      /*} *//* end i1 */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    } /* end j1 */
   }    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   for(cptcov=1;cptcov<=i2;cptcov++){    /*free_vector(pp,1,nlstate);*/
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       k=k+1;  }  /* End of prevalence */
       fprintf(ficrespop,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {  /************* Waves Concatenation ***************/
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }  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)
       fprintf(ficrespop,"******\n");  {
       fprintf(ficrespop,"# Age");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);       Death is a valid wave (if date is known).
       if (popforecast==1)  fprintf(ficrespop," [Population]");       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]
       for (cpt=0; cpt<=0;cpt++) {       and mw[mi+1][i]. dh depends on stepm.
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);         */
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int i, mi, m;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           nhstepm = nhstepm/hstepm;       double sum=0., jmean=0.;*/
              int first;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int j, k=0,jk, ju, jl;
           oldm=oldms;savm=savms;    double sum=0.;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      first=0;
            jmin=1e+5;
           for (h=0; h<=nhstepm; h++){    jmax=-1;
             if (h==(int) (calagedate+YEARM*cpt)) {    jmean=0.;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    for(i=1; i<=imx; i++){
             }      mi=0;
             for(j=1; j<=nlstate+ndeath;j++) {      m=firstpass;
               kk1=0.;kk2=0;      while(s[m][i] <= nlstate){
               for(i=1; i<=nlstate;i++) {                      if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
                 if (mobilav==1)          mw[++mi][i]=m;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if(m >=lastpass)
                 else {          break;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        else
                 }          m++;
               }      }/* end while */
               if (h==(int)(calagedate+12*cpt)){      if (s[m][i] > nlstate){
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;        mi++;     /* Death is another wave */
                   /*fprintf(ficrespop," %.3f", kk1);        /* if(mi==0)  never been interviewed correctly before death */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/           /* Only death is a correct wave */
               }        mw[mi][i]=m;
             }      }
             for(i=1; i<=nlstate;i++){  
               kk1=0.;      wav[i]=mi;
                 for(j=1; j<=nlstate;j++){      if(mi==0){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        nbwarn++;
                 }        if(first==0){
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
             }          first=1;
         }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        if(first==1){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end mi==0 */
         }    } /* End individuals */
       }  
      for(i=1; i<=imx; i++){
   /******/      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          dh[mi][i]=1;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          else{
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            if (agedc[i] < 2*AGESUP) {
           nhstepm = nhstepm/hstepm;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                        if(j==0) j=1;  /* Survives at least one month after exam */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              else if(j<0){
           oldm=oldms;savm=savms;                nberr++;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           for (h=0; h<=nhstepm; h++){                j=1; /* Temporary Dangerous patch */
             if (h==(int) (calagedate+YEARM*cpt)) {                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             for(j=1; j<=nlstate+ndeath;j++) {              }
               kk1=0.;kk2=0;              k=k+1;
               for(i=1; i<=nlstate;i++) {                            if (j >= jmax){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                    jmax=j;
               }                ijmax=i;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);              }
             }              if (j <= jmin){
           }                jmin=j;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                ijmin=i;
         }              }
       }              sum=sum+j;
    }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
           else{
   if (popforecast==1) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     free_ivector(popage,0,AGESUP);  /*        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]); */
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);            k=k+1;
   }            if (j >= jmax) {
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              jmax=j;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              ijmax=i;
   fclose(ficrespop);            }
 }            else if (j <= jmin){
               jmin=j;
 /***********************************************/              ijmin=i;
 /**************** Main Program *****************/            }
 /***********************************************/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
 int main(int argc, char *argv[])            if(j<0){
 {              nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;              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]);
   double agedeb, agefin,hf;            }
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;            sum=sum+j;
           }
   double fret;          jk= j/stepm;
   double **xi,tmp,delta;          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
   double dum; /* Dummy variable */          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   double ***p3mat;            if(jl==0){
   int *indx;              dh[mi][i]=jk;
   char line[MAXLINE], linepar[MAXLINE];              bh[mi][i]=0;
   char title[MAXLINE];            }else{ /* We want a negative bias in order to only have interpolation ie
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];                    * to avoid the price of an extra matrix product in likelihood */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];            }
           }else{
   char filerest[FILENAMELENGTH];            if(jl <= -ju){
   char fileregp[FILENAMELENGTH];              dh[mi][i]=jk;
   char popfile[FILENAMELENGTH];              bh[mi][i]=jl;       /* bias is positive if real duration
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                                   * is higher than the multiple of stepm and negative otherwise.
   int firstobs=1, lastobs=10;                                   */
   int sdeb, sfin; /* Status at beginning and end */            }
   int c,  h , cpt,l;            else{
   int ju,jl, mi;              dh[mi][i]=jk+1;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              bh[mi][i]=ju;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            }
   int mobilav=0,popforecast=0;            if(dh[mi][i]==0){
   int hstepm, nhstepm;              dh[mi][i]=1; /* At least one step */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;              bh[mi][i]=ju; /* At least one step */
               /*  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);*/
   double bage, fage, age, agelim, agebase;            }
   double ftolpl=FTOL;          } /* end if mle */
   double **prlim;        }
   double *severity;      } /* end wave */
   double ***param; /* Matrix of parameters */    }
   double  *p;    jmean=sum/k;
   double **matcov; /* Matrix of covariance */    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);
   double ***delti3; /* Scale */    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);
   double *delti; /* Scale */   }
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  /*********** Tricode ****************************/
   double *epj, vepp;  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   double kk1, kk2;  {
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    /**< 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 
     /* Boring subroutine which should only output nbcode[Tvar[j]][k]
   char version[80]="Imach version 0.8a1, June 2003, INED-EUROREVES ";     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   char *alph[]={"a","a","b","c","d","e"}, str[4];    /* nbcode[Tvar[j]][1]= 
     */
   
   char z[1]="c", occ;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
 #include <sys/time.h>    int modmaxcovj=0; /* Modality max of covariates j */
 #include <time.h>    int cptcode=0; /* Modality max of covariates j */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int modmincovj=0; /* Modality min of covariates j */
    
   /* long total_usecs;  
   struct timeval start_time, end_time;    cptcoveff=0; 
     
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   getcwd(pathcd, size);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   printf("\n%s",version);    /* Loop on covariates without age and products */
   if(argc <=1){    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
     printf("\nEnter the parameter file name: ");      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
     scanf("%s",pathtot);                                 modality of this covariate Vj*/ 
   }        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
   else{                                      * If product of Vn*Vm, still boolean *:
     strcpy(pathtot,argv[1]);                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   }                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   /*cygwin_split_path(pathtot,path,optionfile);                                        modality of the nth covariate of individual i. */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        if (ij > modmaxcovj)
   /* cutv(path,optionfile,pathtot,'\\');*/          modmaxcovj=ij; 
         else if (ij < modmincovj) 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          modmincovj=ij; 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        if ((ij < -1) && (ij > NCOVMAX)){
   chdir(path);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   replace(pathc,path);          exit(1);
         }else
 /*-------- arguments in the command line --------*/        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   strcpy(fileres,"r");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   strcat(fileres, optionfilefiname);        /* getting the maximum value of the modality of the covariate
   strcat(fileres,".txt");    /* Other files have txt extension */           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
            female is 1, then modmaxcovj=1.*/
   /*---------arguments file --------*/      }
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      cptcode=modmaxcovj;
     printf("Problem with optionfile %s\n",optionfile);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     goto end;     /*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]);
   strcpy(filereso,"o");        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
   strcat(filereso,fileres);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
   if((ficparo=fopen(filereso,"w"))==NULL) {        }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        /* 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 */
       } /* Ndum[-1] number of undefined modalities */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     ungetc(c,ficpar);      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
     fgets(line, MAXLINE, ficpar);      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
     puts(line);         modmincovj=3; modmaxcovj = 7;
     fputs(line,ficparo);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
   }         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
   ungetc(c,ficpar);         variables V1_1 and V1_2.
          nbcode[Tvar[j]][ij]=k;
   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);         nbcode[Tvar[j]][1]=0;
   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);         nbcode[Tvar[j]][2]=1;
   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);         nbcode[Tvar[j]][3]=2;
 while((c=getc(ficpar))=='#' && c!= EOF){      */
     ungetc(c,ficpar);      ij=1; /* ij is similar to i but can jumps over null modalities */
     fgets(line, MAXLINE, ficpar);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
     puts(line);        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
     fputs(line,ficparo);          /*recode from 0 */
   }          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   ungetc(c,ficpar);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                         k is a modality. If we have model=V1+V1*sex 
                                           then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   covar=matrix(0,NCOVMAX,1,n);            ij++;
   cptcovn=0;          }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          if (ij > ncodemax[j]) break; 
         }  /* end of loop on */
   ncovmodel=2+cptcovn;      } /* end of loop on modality */ 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
      
   /* Read guess parameters */   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     ungetc(c,ficpar);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
     fgets(line, MAXLINE, ficpar);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     puts(line);     Ndum[ij]++; 
     fputs(line,ficparo);   } 
   }  
   ungetc(c,ficpar);   ij=1;
     for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
     for(i=1; i <=nlstate; i++)     if((Ndum[i]!=0) && (i<=ncovcol)){
     for(j=1; j <=nlstate+ndeath-1; j++){       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
       fscanf(ficpar,"%1d%1d",&i1,&j1);       Tvaraff[ij]=i; /*For printing (unclear) */
       fprintf(ficparo,"%1d%1d",i1,j1);       ij++;
       printf("%1d%1d",i,j);     }else
       for(k=1; k<=ncovmodel;k++){         Tvaraff[ij]=0;
         fscanf(ficpar," %lf",&param[i][j][k]);   }
         printf(" %lf",param[i][j][k]);   ij--;
         fprintf(ficparo," %lf",param[i][j][k]);   cptcoveff=ij; /*Number of total covariates*/
       }  
       fscanf(ficpar,"\n");  }
       printf("\n");  
       fprintf(ficparo,"\n");  
     }  /*********** Health Expectancies ****************/
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
   p=param[1][1];  {
      /* Health expectancies, no variances */
   /* Reads comments: lines beginning with '#' */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   while((c=getc(ficpar))=='#' && c!= EOF){    int nhstepma, nstepma; /* Decreasing with age */
     ungetc(c,ficpar);    double age, agelim, hf;
     fgets(line, MAXLINE, ficpar);    double ***p3mat;
     puts(line);    double eip;
     fputs(line,ficparo);  
   }    pstamp(ficreseij);
   ungetc(c,ficpar);    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");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for(i=1; i<=nlstate;i++){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      for(j=1; j<=nlstate;j++){
   for(i=1; i <=nlstate; i++){        fprintf(ficreseij," e%1d%1d ",i,j);
     for(j=1; j <=nlstate+ndeath-1; j++){      }
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(ficreseij," e%1d. ",i);
       printf("%1d%1d",i,j);    }
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficreseij,"\n");
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);    
         printf(" %le",delti3[i][j][k]);    if(estepm < stepm){
         fprintf(ficparo," %le",delti3[i][j][k]);      printf ("Problem %d lower than %d\n",estepm, stepm);
       }    }
       fscanf(ficpar,"\n");    else  hstepm=estepm;   
       printf("\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
       fprintf(ficparo,"\n");     * 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 
   delti=delti3[1][1];     * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   /* Reads comments: lines beginning with '#' */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   while((c=getc(ficpar))=='#' && c!= EOF){     * to compare the new estimate of Life expectancy with the same linear 
     ungetc(c,ficpar);     * hypothesis. A more precise result, taking into account a more precise
     fgets(line, MAXLINE, ficpar);     * curvature will be obtained if estepm is as small as stepm. */
     puts(line);  
     fputs(line,ficparo);    /* For example we decided to compute the life expectancy with the smallest unit */
   }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   ungetc(c,ficpar);       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   matcov=matrix(1,npar,1,npar);       Look at hpijx to understand the reason of that which relies in memory size
   for(i=1; i <=npar; i++){       and note for a fixed period like estepm months */
     fscanf(ficpar,"%s",&str);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     printf("%s",str);       survival function given by stepm (the optimization length). Unfortunately it
     fprintf(ficparo,"%s",str);       means that if the survival funtion is printed only each two years of age and if
     for(j=1; j <=i; j++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fscanf(ficpar," %le",&matcov[i][j]);       results. So we changed our mind and took the option of the best precision.
       printf(" %.5le",matcov[i][j]);    */
       fprintf(ficparo," %.5le",matcov[i][j]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     }  
     fscanf(ficpar,"\n");    agelim=AGESUP;
     printf("\n");    /* If stepm=6 months */
     fprintf(ficparo,"\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   for(i=1; i <=npar; i++)      
     for(j=i+1;j<=npar;j++)  /* nhstepm age range expressed in number of stepm */
       matcov[i][j]=matcov[j][i];    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   printf("\n");    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */    for (age=bage; age<=fage; age ++){ 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      strcat(rfileres,".");    /* */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      /* if (stepm >= YEARM) hstepm=1;*/
     if((ficres =fopen(rfileres,"w"))==NULL) {      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     }      /* If stepm=6 months */
     fprintf(ficres,"#%s\n",version);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
             in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     /*-------- data file ----------*/      
     if((fic=fopen(datafile,"r"))==NULL)    {      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       printf("Problem with datafile: %s\n", datafile);goto end;      
     }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
     n= lastobs;      printf("%d|",(int)age);fflush(stdout);
     severity = vector(1,maxwav);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     outcome=imatrix(1,maxwav+1,1,n);      
     num=ivector(1,n);      /* Computing expectancies */
     moisnais=vector(1,n);      for(i=1; i<=nlstate;i++)
     annais=vector(1,n);        for(j=1; j<=nlstate;j++)
     moisdc=vector(1,n);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     andc=vector(1,n);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     agedc=vector(1,n);            
     cod=ivector(1,n);            /* 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]);*/
     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);      fprintf(ficreseij,"%3.0f",age );
     s=imatrix(1,maxwav+1,1,n);      for(i=1; i<=nlstate;i++){
     adl=imatrix(1,maxwav+1,1,n);            eip=0;
     tab=ivector(1,NCOVMAX);        for(j=1; j<=nlstate;j++){
     ncodemax=ivector(1,8);          eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     i=1;        }
     while (fgets(line, MAXLINE, fic) != NULL)    {        fprintf(ficreseij,"%9.4f", eip );
       if ((i >= firstobs) && (i <=lastobs)) {      }
              fprintf(ficreseij,"\n");
         for (j=maxwav;j>=1;j--){      
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    }
           strcpy(line,stra);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    printf("\n");
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficlog,"\n");
         }    
          }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  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[] )
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  {
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    */
         for (j=ncovcol;j>=1;j--){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int nhstepma, nstepma; /* Decreasing with age */
         }    double age, agelim, hf;
         num[i]=atol(stra);    double ***p3matp, ***p3matm, ***varhe;
            double **dnewm,**doldm;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    double *xp, *xm;
           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;}*/    double **gp, **gm;
     double ***gradg, ***trgradg;
         i=i+1;    int theta;
       }  
     }    double eip, vip;
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   imx=i-1; /* Number of individuals */    xp=vector(1,npar);
     xm=vector(1,npar);
   /* for (i=1; i<=imx; i++){    dnewm=matrix(1,nlstate*nlstate,1,npar);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    pstamp(ficresstdeij);
     }*/    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
    /*  for (i=1; i<=imx; i++){    fprintf(ficresstdeij,"# Age");
      if (s[4][i]==9)  s[4][i]=-1;    for(i=1; i<=nlstate;i++){
      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]));}*/      for(j=1; j<=nlstate;j++)
          fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
        fprintf(ficresstdeij," e%1d. ",i);
   /* Calculation of the number of parameter from char model*/    }
   Tvar=ivector(1,15);    fprintf(ficresstdeij,"\n");
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);    pstamp(ficrescveij);
   Tvard=imatrix(1,15,1,2);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   Tage=ivector(1,15);          fprintf(ficrescveij,"# Age");
        for(i=1; i<=nlstate;i++)
   if (strlen(model) >1){      for(j=1; j<=nlstate;j++){
     j=0, j1=0, k1=1, k2=1;        cptj= (j-1)*nlstate+i;
     j=nbocc(model,'+');        for(i2=1; i2<=nlstate;i2++)
     j1=nbocc(model,'*');          for(j2=1; j2<=nlstate;j2++){
     cptcovn=j+1;            cptj2= (j2-1)*nlstate+i2;
     cptcovprod=j1;            if(cptj2 <= cptj)
                  fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     strcpy(modelsav,model);          }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      }
       printf("Error. Non available option model=%s ",model);    fprintf(ficrescveij,"\n");
       goto end;    
     }    if(estepm < stepm){
          printf ("Problem %d lower than %d\n",estepm, stepm);
     for(i=(j+1); i>=1;i--){    }
       cutv(stra,strb,modelsav,'+');    else  hstepm=estepm;   
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    /* We compute the life expectancy from trapezoids spaced every estepm months
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/     * This is mainly to measure the difference between two models: for example
       /*scanf("%d",i);*/     * if stepm=24 months pijx are given only every 2 years and by summing them
       if (strchr(strb,'*')) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
         cutv(strd,strc,strb,'*');     * progression in between and thus overestimating or underestimating according
         if (strcmp(strc,"age")==0) {     * to the curvature of the survival function. If, for the same date, we 
           cptcovprod--;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           cutv(strb,stre,strd,'V');     * to compare the new estimate of Life expectancy with the same linear 
           Tvar[i]=atoi(stre);     * hypothesis. A more precise result, taking into account a more precise
           cptcovage++;     * curvature will be obtained if estepm is as small as stepm. */
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/    /* For example we decided to compute the life expectancy with the smallest unit */
         }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         else if (strcmp(strd,"age")==0) {       nhstepm is the number of hstepm from age to agelim 
           cptcovprod--;       nstepm is the number of stepm from age to agelin. 
           cutv(strb,stre,strc,'V');       Look at hpijx to understand the reason of that which relies in memory size
           Tvar[i]=atoi(stre);       and note for a fixed period like estepm months */
           cptcovage++;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           Tage[cptcovage]=i;       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
         else {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           cutv(strb,stre,strc,'V');       results. So we changed our mind and took the option of the best precision.
           Tvar[i]=ncovcol+k1;    */
           cutv(strb,strc,strd,'V');    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);    /* If stepm=6 months */
           Tvard[k1][2]=atoi(stre);    /* nhstepm age range expressed in number of stepm */
           Tvar[cptcovn+k2]=Tvard[k1][1];    agelim=AGESUP;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
           for (k=1; k<=lastobs;k++)    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    /* if (stepm >= YEARM) hstepm=1;*/
           k1++;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           k2=k2+2;    
         }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       else {    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
        /*  scanf("%d",i);*/    gp=matrix(0,nhstepm,1,nlstate*nlstate);
       cutv(strd,strc,strb,'V');    gm=matrix(0,nhstepm,1,nlstate*nlstate);
       Tvar[i]=atoi(strc);  
       }    for (age=bage; age<=fage; age ++){ 
       strcpy(modelsav,stra);        nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         scanf("%d",i);*/      /* if (stepm >= YEARM) hstepm=1;*/
     }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
 }  
        /* If stepm=6 months */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   printf("cptcovprod=%d ", cptcovprod);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   scanf("%d ",i);*/      
     fclose(fic);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
     /*  if(mle==1){*/      /* Computing  Variances of health expectancies */
     if (weightopt != 1) { /* Maximisation without weights*/      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       for(i=1;i<=n;i++) weight[i]=1.0;         decrease memory allocation */
     }      for(theta=1; theta <=npar; theta++){
     /*-calculation of age at interview from date of interview and age at death -*/        for(i=1; i<=npar; i++){ 
     agev=matrix(1,maxwav,1,imx);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
     for (i=1; i<=imx; i++) {        }
       for(m=2; (m<= maxwav); m++) {        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
          anint[m][i]=9999;    
          s[m][i]=-1;        for(j=1; j<= nlstate; j++){
        }          for(i=1; i<=nlstate; i++){
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;            for(h=0; h<=nhstepm-1; h++){
       }              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     }              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
     for (i=1; i<=imx; i++)  {          }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        }
       for(m=1; (m<= maxwav); m++){       
         if(s[m][i] >0){        for(ij=1; ij<= nlstate*nlstate; ij++)
           if (s[m][i] >= nlstate+1) {          for(h=0; h<=nhstepm-1; h++){
             if(agedc[i]>0)            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
               if(moisdc[i]!=99 && andc[i]!=9999)          }
                 agev[m][i]=agedc[i];      }/* End theta */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      
            else {      
               if (andc[i]!=9999){      for(h=0; h<=nhstepm-1; h++)
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        for(j=1; j<=nlstate*nlstate;j++)
               agev[m][i]=-1;          for(theta=1; theta <=npar; theta++)
               }            trgradg[h][j][theta]=gradg[h][theta][j];
             }      
           }  
           else if(s[m][i] !=9){ /* Should no more exist */       for(ij=1;ij<=nlstate*nlstate;ij++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        for(ji=1;ji<=nlstate*nlstate;ji++)
             if(mint[m][i]==99 || anint[m][i]==9999)          varhe[ij][ji][(int)age] =0.;
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){       printf("%d|",(int)age);fflush(stdout);
               agemin=agev[m][i];       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       for(h=0;h<=nhstepm-1;h++){
             }        for(k=0;k<=nhstepm-1;k++){
             else if(agev[m][i] >agemax){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
               agemax=agev[m][i];          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          for(ij=1;ij<=nlstate*nlstate;ij++)
             }            for(ji=1;ji<=nlstate*nlstate;ji++)
             /*agev[m][i]=anint[m][i]-annais[i];*/              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
             /*   agev[m][i] = age[i]+2*m;*/        }
           }      }
           else { /* =9 */  
             agev[m][i]=1;      /* Computing expectancies */
             s[m][i]=-1;      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           }      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++)
         else /*= 0 Unknown */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           agev[m][i]=1;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
       }            
                /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     }  
     for (i=1; i<=imx; i++)  {          }
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {      fprintf(ficresstdeij,"%3.0f",age );
           printf("Error: Wrong value in nlstate or ndeath\n");        for(i=1; i<=nlstate;i++){
           goto end;        eip=0.;
         }        vip=0.;
       }        for(j=1; j<=nlstate;j++){
     }          eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     free_vector(severity,1,maxwav);        }
     free_imatrix(outcome,1,maxwav+1,1,n);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     free_vector(moisnais,1,n);      }
     free_vector(annais,1,n);      fprintf(ficresstdeij,"\n");
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/      fprintf(ficrescveij,"%3.0f",age );
     free_vector(moisdc,1,n);      for(i=1; i<=nlstate;i++)
     free_vector(andc,1,n);        for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
              for(i2=1; i2<=nlstate;i2++)
     wav=ivector(1,imx);            for(j2=1; j2<=nlstate;j2++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              cptj2= (j2-1)*nlstate+i2;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              if(cptj2 <= cptj)
                    fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     /* Concatenates waves */            }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        }
       fprintf(ficrescveij,"\n");
      
       Tcode=ivector(1,100);    }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       ncodemax[1]=1;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
          free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
    codtab=imatrix(1,100,1,10);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    h=0;    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    m=pow(2,cptcoveff);    printf("\n");
      fprintf(ficlog,"\n");
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    free_vector(xm,1,npar);
        for(j=1; j <= ncodemax[k]; j++){    free_vector(xp,1,npar);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
            h++;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  }
          }  
        }  /************ 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[])
    }  {
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    /* Variance of health expectancies */
       codtab[1][2]=1;codtab[2][2]=2; */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    /* for(i=1; i <=m ;i++){    /* double **newm;*/
       for(k=1; k <=cptcovn; k++){    double **dnewm,**doldm;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    double **dnewmp,**doldmp;
       }    int i, j, nhstepm, hstepm, h, nstepm ;
       printf("\n");    int k, cptcode;
       }    double *xp;
       scanf("%d",i);*/    double **gp, **gm;  /* for var eij */
        double ***gradg, ***trgradg; /*for var eij */
    /* Calculates basic frequencies. Computes observed prevalence at single age    double **gradgp, **trgradgp; /* for var p point j */
        and prints on file fileres'p'. */    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        double ***p3mat;
        double age,agelim, hf;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***mobaverage;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int theta;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char digit[4];
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char digitp[25];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
          char fileresprobmorprev[FILENAMELENGTH];
     /* 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] */    if(popbased==1){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
     if(mle==1){      else strcpy(digitp,"-populbased-nomobil-");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    }
     }    else 
          strcpy(digitp,"-stablbased-");
     /*--------- 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);    if (mobilav!=0) {
        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
    jk=1;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
    printf("# 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)    strcpy(fileresprobmorprev,"prmorprev"); 
          {    sprintf(digit,"%-d",ij);
            printf("%d%d ",i,k);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
            fprintf(ficres,"%1d%1d ",i,k);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
            for(j=1; j <=ncovmodel; j++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
              printf("%f ",p[jk]);    strcat(fileresprobmorprev,fileres);
              fprintf(ficres,"%f ",p[jk]);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
              jk++;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
            }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
            printf("\n");    }
            fprintf(ficres,"\n");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          }   
      }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    }    pstamp(ficresprobmorprev);
  if(mle==1){    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);
     /* Computing hessian and covariance matrix */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     ftolhess=ftol; /* Usually correct */    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     hesscov(matcov, p, npar, delti, ftolhess, func);      fprintf(ficresprobmorprev," p.%-d SE",j);
  }      for(i=1; i<=nlstate;i++)
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     printf("# Scales (for hessian or gradient estimation)\n");    }  
      for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficresprobmorprev,"\n");
       for(j=1; j <=nlstate+ndeath; j++){    fprintf(ficgp,"\n# Routine varevsij");
         if (j!=i) {    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
           fprintf(ficres,"%1d%1d",i,j);    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
           printf("%1d%1d",i,j);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           for(k=1; k<=ncovmodel;k++){  /*   } */
             printf(" %.5e",delti[jk]);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             fprintf(ficres," %.5e",delti[jk]);    pstamp(ficresvij);
             jk++;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
           }    if(popbased==1)
           printf("\n");      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
           fprintf(ficres,"\n");    else
         }      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
       }    fprintf(ficresvij,"# Age");
      }    for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
     k=1;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     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");    fprintf(ficresvij,"\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");  
     for(i=1;i<=npar;i++){    xp=vector(1,npar);
       /*  if (k>nlstate) k=1;    dnewm=matrix(1,nlstate,1,npar);
       i1=(i-1)/(ncovmodel*nlstate)+1;    doldm=matrix(1,nlstate,1,nlstate);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       for(j=1; j<=i;j++){    gpp=vector(nlstate+1,nlstate+ndeath);
         fprintf(ficres," %.5e",matcov[i][j]);    gmp=vector(nlstate+1,nlstate+ndeath);
         printf(" %.5e",matcov[i][j]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       }    
       fprintf(ficres,"\n");    if(estepm < stepm){
       printf("\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
       k++;    }
     }    else  hstepm=estepm;   
        /* For example we decided to compute the life expectancy with the smallest unit */
     while((c=getc(ficpar))=='#' && c!= EOF){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       ungetc(c,ficpar);       nhstepm is the number of hstepm from age to agelim 
       fgets(line, MAXLINE, ficpar);       nstepm is the number of stepm from age to agelin. 
       puts(line);       Look at function hpijx to understand why (it is linked to memory size questions) */
       fputs(line,ficparo);    /* 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
     ungetc(c,ficpar);       means that if the survival funtion is printed every two years of age and if
     estepm=0;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);       results. So we changed our mind and took the option of the best precision.
     if (estepm==0 || estepm < stepm) estepm=stepm;    */
     if (fage <= 2) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       bage = ageminpar;    agelim = AGESUP;
       fage = agemaxpar;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
     while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      for(theta=1; theta <=npar; theta++){
     puts(line);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     fputs(line,ficparo);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
   ungetc(c,ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);  
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        if (popbased==1) {
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          if(mobilav ==0){
                  for(i=1; i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              prlim[i][i]=probs[(int)age][i][ij];
     ungetc(c,ficpar);          }else{ /* mobilav */ 
     fgets(line, MAXLINE, ficpar);            for(i=1; i<=nlstate;i++)
     puts(line);              prlim[i][i]=mobaverage[(int)age][i][ij];
     fputs(line,ficparo);          }
   }        }
   ungetc(c,ficpar);    
          for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   fscanf(ficpar,"pop_based=%d\n",&popbased);        }
   fprintf(ficparo,"pop_based=%d\n",popbased);          /* This for computing probability of death (h=1 means
   fprintf(ficres,"pop_based=%d\n",popbased);             computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   while((c=getc(ficpar))=='#' && c!= EOF){        */
     ungetc(c,ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fgets(line, MAXLINE, ficpar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     puts(line);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     fputs(line,ficparo);        }    
   }        /* end probability of death */
   ungetc(c,ficpar);  
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   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);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 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);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 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);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
 while((c=getc(ficpar))=='#' && c!= EOF){          if(mobilav ==0){
     ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);              prlim[i][i]=probs[(int)age][i][ij];
     puts(line);          }else{ /* mobilav */ 
     fputs(line,ficparo);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
   ungetc(c,ficpar);          }
         }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   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++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
 /*------------ gnuplot -------------*/        }
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);        /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
 /*------------ free_vector  -------------*/           as a weighted average of prlim.
  chdir(path);        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
  free_ivector(wav,1,imx);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          }    
  free_ivector(num,1,n);        /* end probability of death */
  free_vector(agedc,1,n);  
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        for(j=1; j<= nlstate; j++) /* vareij */
  fclose(ficparo);          for(h=0; h<=nhstepm; h++){
  fclose(ficres);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
 /*--------- index.htm --------*/  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
    
   /*--------------- Prevalence limit --------------*/      } /* End theta */
    
   strcpy(filerespl,"pl");      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      for(h=0; h<=nhstepm; h++) /* veij */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        for(j=1; j<=nlstate;j++)
   }          for(theta=1; theta <=npar; theta++)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            trgradg[h][j][theta]=gradg[h][theta][j];
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(theta=1; theta <=npar; theta++)
   fprintf(ficrespl,"\n");          trgradgp[j][theta]=gradgp[theta][j];
      
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1;i<=nlstate;i++)
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1;j<=nlstate;j++)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          vareij[i][j][(int)age] =0.;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;      for(h=0;h<=nhstepm;h++){
   agebase=ageminpar;        for(k=0;k<=nhstepm;k++){
   agelim=agemaxpar;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   ftolpl=1.e-10;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   i1=cptcoveff;          for(i=1;i<=nlstate;i++)
   if (cptcovn < 1){i1=1;}            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
         k=k+1;    
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      /* pptj */
         fprintf(ficrespl,"\n#******");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         for(j=1;j<=cptcoveff;j++)      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         fprintf(ficrespl,"******\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
                  varppt[j][i]=doldmp[j][i];
         for (age=agebase; age<=agelim; age++){      /* end ppptj */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      /*  x centered again */
           fprintf(ficrespl,"%.0f",age );      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           for(i=1; i<=nlstate;i++)      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           fprintf(ficrespl," %.5f", prlim[i][i]);   
           fprintf(ficrespl,"\n");      if (popbased==1) {
         }        if(mobilav ==0){
       }          for(i=1; i<=nlstate;i++)
     }            prlim[i][i]=probs[(int)age][i][ij];
   fclose(ficrespl);        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   /*------------- h Pij x at various ages ------------*/            prlim[i][i]=mobaverage[(int)age][i][ij];
          }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {               
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      /* This for computing probability of death (h=1 means
   }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   printf("Computing pij: result on file '%s' \n", filerespij);         as a weighted average of prlim.
        */
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /*if (stepm<=24) stepsize=2;*/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   agelim=AGESUP;      }    
   hstepm=stepsize*YEARM; /* Every year of age */      /* end probability of death */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   k=0;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1; i<=nlstate;i++){
       k=k+1;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         fprintf(ficrespij,"\n#****** ");        }
         for(j=1;j<=cptcoveff;j++)      } 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficresprobmorprev,"\n");
         fprintf(ficrespij,"******\n");  
              fprintf(ficresvij,"%.0f ",age );
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      for(i=1; i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(j=1; j<=nlstate;j++){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           oldm=oldms;savm=savms;      fprintf(ficresvij,"\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        free_matrix(gp,0,nhstepm,1,nlstate);
           fprintf(ficrespij,"# Age");      free_matrix(gm,0,nhstepm,1,nlstate);
           for(i=1; i<=nlstate;i++)      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
             for(j=1; j<=nlstate+ndeath;j++)      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
               fprintf(ficrespij," %1d-%1d",i,j);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");    } /* End age */
            for (h=0; h<=nhstepm; h++){    free_vector(gpp,nlstate+1,nlstate+ndeath);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    free_vector(gmp,nlstate+1,nlstate+ndeath);
             for(i=1; i<=nlstate;i++)    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
               for(j=1; j<=nlstate+ndeath;j++)    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
             fprintf(ficrespij,"\n");    /* 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)\";");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           fprintf(ficrespij,"\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
   }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    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);
   fclose(ficrespij);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   /*---------- Forecasting ------------------*/    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    free_vector(xp,1,npar);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    free_matrix(doldm,1,nlstate,1,nlstate);
   }    free_matrix(dnewm,1,nlstate,1,npar);
   else{    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     erreur=108;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     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);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficresprobmorprev);
     fflush(ficgp);
   /*---------- Health expectancies and variances ------------*/    fflush(fichtm); 
   }  /* end varevsij */
   strcpy(filerest,"t");  
   strcat(filerest,fileres);  /************ Variance of prevlim ******************/
   if((ficrest=fopen(filerest,"w"))==NULL) {  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[])
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  {
   }    /* Variance of prevalence limit */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
   strcpy(filerese,"e");    int i, j, nhstepm, hstepm;
   strcat(filerese,fileres);    int k, cptcode;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    double *xp;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double *gp, *gm;
   }    double **gradg, **trgradg;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    double age,agelim;
     int theta;
  strcpy(fileresv,"v");    
   strcat(fileresv,fileres);    pstamp(ficresvpl);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    fprintf(ficresvpl,"# Age");
   }    for(i=1; i<=nlstate;i++)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        fprintf(ficresvpl," %1d-%1d",i,i);
   calagedate=-1;    fprintf(ficresvpl,"\n");
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
     xp=vector(1,npar);
   k=0;    dnewm=matrix(1,nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    doldm=matrix(1,nlstate,1,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    hstepm=1*YEARM; /* Every year of age */
       fprintf(ficrest,"\n#****** ");    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       for(j=1;j<=cptcoveff;j++)    agelim = AGESUP;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficrest,"******\n");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       fprintf(ficreseij,"\n#****** ");      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       for(j=1;j<=cptcoveff;j++)      gradg=matrix(1,npar,1,nlstate);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      gp=vector(1,nlstate);
       fprintf(ficreseij,"******\n");      gm=vector(1,nlstate);
   
       fprintf(ficresvij,"\n#****** ");      for(theta=1; theta <=npar; theta++){
       for(j=1;j<=cptcoveff;j++)        for(i=1; i<=npar; i++){ /* Computes gradient */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficresvij,"******\n");        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for(i=1;i<=nlstate;i++)
       oldm=oldms;savm=savms;          gp[i] = prlim[i][i];
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        
          for(i=1; i<=npar; i++) /* Computes gradient */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       oldm=oldms;savm=savms;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        for(i=1;i<=nlstate;i++)
              gm[i] = prlim[i][i];
   
          for(i=1;i<=nlstate;i++)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      } /* End theta */
       fprintf(ficrest,"\n");  
       trgradg =matrix(1,nlstate,1,npar);
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){      for(j=1; j<=nlstate;j++)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(theta=1; theta <=npar; theta++)
         if (popbased==1) {          trgradg[j][theta]=gradg[theta][j];
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][k];      for(i=1;i<=nlstate;i++)
         }        varpl[i][(int)age] =0.;
              matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         fprintf(ficrest," %4.0f",age);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      for(i=1;i<=nlstate;i++)
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      fprintf(ficresvpl,"%.0f ",age );
           }      for(i=1; i<=nlstate;i++)
           epj[nlstate+1] +=epj[j];        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         }      fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
         for(i=1, vepp=0.;i <=nlstate;i++)      free_vector(gm,1,nlstate);
           for(j=1;j <=nlstate;j++)      free_matrix(gradg,1,npar,1,nlstate);
             vepp += vareij[i][j][(int)age];      free_matrix(trgradg,1,nlstate,1,npar);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    } /* End age */
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    free_vector(xp,1,npar);
         }    free_matrix(doldm,1,nlstate,1,npar);
         fprintf(ficrest,"\n");    free_matrix(dnewm,1,nlstate,1,nlstate);
       }  
     }  }
   }  
 free_matrix(mint,1,maxwav,1,n);  /************ Variance of one-step probabilities  ******************/
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  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[])
     free_vector(weight,1,n);  {
   fclose(ficreseij);    int i, j=0,  i1, k1, l1, t, tj;
   fclose(ficresvij);    int k2, l2, j1,  z1;
   fclose(ficrest);    int k=0,l, cptcode;
   fclose(ficpar);    int first=1, first1, first2;
   free_vector(epj,1,nlstate+1);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      double **dnewm,**doldm;
   /*------- Variance limit prevalence------*/      double *xp;
     double *gp, *gm;
   strcpy(fileresvpl,"vpl");    double **gradg, **trgradg;
   strcat(fileresvpl,fileres);    double **mu;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    double age,agelim, cov[NCOVMAX+1];
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     exit(0);    int theta;
   }    char fileresprob[FILENAMELENGTH];
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   k=0;    double ***varpij;
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcpy(fileresprob,"prob"); 
       k=k+1;    strcat(fileresprob,fileres);
       fprintf(ficresvpl,"\n#****** ");    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       for(j=1;j<=cptcoveff;j++)      printf("Problem with resultfile: %s\n", fileresprob);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       fprintf(ficresvpl,"******\n");    }
          strcpy(fileresprobcov,"probcov"); 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    strcat(fileresprobcov,fileres);
       oldm=oldms;savm=savms;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      printf("Problem with resultfile: %s\n", fileresprobcov);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
  }    }
     strcpy(fileresprobcor,"probcor"); 
   fclose(ficresvpl);    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   /*---------- End : free ----------------*/      printf("Problem with resultfile: %s\n", fileresprobcor);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    pstamp(ficresprob);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
   free_matrix(matcov,1,npar,1,npar);    pstamp(ficresprobcov);
   free_vector(delti,1,npar);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   free_matrix(agev,1,maxwav,1,imx);    fprintf(ficresprobcov,"# Age");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   if(erreur >0)    fprintf(ficresprobcor,"# Age");
     printf("End of Imach with error or warning %d\n",erreur);  
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   /*printf("Total time was %d uSec.\n", total_usecs);*/        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   /*------ End -----------*/        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
  end:    fprintf(ficresprobcov,"\n");
   /* chdir(pathcd);*/    fprintf(ficresprobcor,"\n");
  /*system("wgnuplot graph.plt");*/   */
  /*system("../gp37mgw/wgnuplot graph.plt");*/    xp=vector(1,npar);
  /*system("cd ../gp37mgw");*/    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
  strcpy(plotcmd,GNUPLOTPROGRAM);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
  strcat(plotcmd," ");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
  strcat(plotcmd,optionfilegnuplot);    first=1;
  system(plotcmd);    fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
  /*#ifdef windows*/    fprintf(fichtm,"\n");
   while (z[0] != 'q') {  
     /* chdir(path); */    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     scanf("%s",z);    file %s<br>\n",optionfilehtmcov);
     if (z[0] == 'c') system("./imach");    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     else if (z[0] == 'e') system(optionfilehtm);  and drawn. It helps understanding how is the covariance between two incidences.\
     else if (z[0] == 'g') system(plotcmd);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     else if (z[0] == 'q') exit(0);    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 \
   /*#endif */  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
 }  standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.41.2.2  
changed lines
  Added in v.1.148


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