Diff for /imach/src/imach.c between versions 1.26 and 1.174

version 1.26, 2002/02/27 15:42:00 version 1.174, 2015/01/03 16:15:49
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.174  2015/01/03 16:15:49  brouard
      Summary: Still in cross-compilation
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.173  2015/01/03 12:06:26  brouard
   first survey ("cross") where individuals from different ages are    Summary: trying to detect cross-compilation
   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 1.172  2014/12/27 12:07:47  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.171  2014/12/23 13:26:59  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: Back from Visual C
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Still problem with utsname.h on Windows
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.170  2014/12/23 11:17:12  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: Cleaning some \%% back to %%
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.169  2014/12/22 23:08:31  brouard
   convergence.    Summary: 0.98p
   
   The advantage of this computer programme, compared to a simple    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.168  2014/12/22 15:17:42  brouard
   intermediate interview, the information is lost, but taken into    Summary: update
   account using an interpolation or extrapolation.    
     Revision 1.167  2014/12/22 13:50:56  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: Testing uname and compiler version and if compiled 32 or 64
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Testing on Linux 64
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.166  2014/12/22 11:40:47  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    *** empty log message ***
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    * imach.c (Module): Merging 1.61 to 1.162
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.164  2014/12/16 10:52:11  brouard
            Institut national d'études démographiques, Paris.    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    * imach.c (Module): Merging 1.61 to 1.162
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.163  2014/12/16 10:30:11  brouard
   can be accessed at http://euroreves.ined.fr/imach .    * imach.c (Module): Merging 1.61 to 1.162
   **********************************************************************/  
      Revision 1.162  2014/09/25 11:43:39  brouard
 #include <math.h>    Summary: temporary backup 0.99!
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.1  2014/09/16 11:06:58  brouard
 #include <unistd.h>    Summary: With some code (wrong) for nlopt
   
 #define MAXLINE 256    Author:
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    Revision 1.161  2014/09/15 20:41:41  brouard
 /*#define DEBUG*/    Summary: Problem with macro SQR on Intel compiler
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.160  2014/09/02 09:24:05  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    *** empty log message ***
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.159  2014/09/01 10:34:10  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: WIN32
     Author: Brouard
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.158  2014/08/27 17:11:51  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    *** empty log message ***
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.157  2014/08/27 16:26:55  brouard
 #define YEARM 12. /* Number of months per year */    Summary: Preparing windows Visual studio version
 #define AGESUP 130    Author: Brouard
 #define AGEBASE 40  
     In order to compile on Visual studio, time.h is now correct and time_t
     and tm struct should be used. difftime should be used but sometimes I
 int erreur; /* Error number */    just make the differences in raw time format (time(&now).
 int nvar;    Trying to suppress #ifdef LINUX
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Add xdg-open for __linux in order to open default browser.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.156  2014/08/25 20:10:10  brouard
 int ndeath=1; /* Number of dead states */    *** empty log message ***
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
 int *wav; /* Number of waves for this individuual 0 is possible */    Author: Brouard
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.154  2014/06/20 17:32:08  brouard
 int mle, weightopt;    Summary: Outputs now all graphs of convergence to period prevalence
 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 */    Revision 1.153  2014/06/20 16:45:46  brouard
 double jmean; /* Mean space between 2 waves */    Summary: If 3 live state, convergence to period prevalence on same graph
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Author: Brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Revision 1.152  2014/06/18 17:54:09  brouard
 FILE *ficgp,*ficresprob,*ficpop;    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.151  2014/06/18 16:43:30  brouard
  FILE  *ficresvij;    *** empty log message ***
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.150  2014/06/18 16:42:35  brouard
   char fileresvpl[FILENAMELENGTH];    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.149  2014/06/18 15:51:14  brouard
 #define FTOL 1.0e-10    Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
 #define NRANSI  
 #define ITMAX 200    Revision 1.148  2014/06/17 17:38:48  brouard
     Summary: Nothing new
 #define TOL 2.0e-4    Author: Brouard
   
 #define CGOLD 0.3819660    Just a new packaging for OS/X version 0.98nS
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.146  2014/06/16 10:20:28  brouard
 #define TINY 1.0e-20    Summary: Merge
     Author: Brouard
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Merge, before building revised version.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.145  2014/06/10 21:23:15  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Summary: Debugging with valgrind
 #define rint(a) floor(a+0.5)    Author: Nicolas Brouard
   
 static double sqrarg;    Lot of changes in order to output the results with some covariates
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    After the Edimburgh REVES conference 2014, it seems mandatory to
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    improve the code.
     No more memory valgrind error but a lot has to be done in order to
 int imx;    continue the work of splitting the code into subroutines.
 int stepm;    Also, decodemodel has been improved. Tricode is still not
 /* Stepm, step in month: minimum step interpolation*/    optimal. nbcode should be improved. Documentation has been added in
     the source code.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.143  2014/01/26 09:45:38  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 double *weight;  
 int **s; /* Status */    Revision 1.142  2014/01/26 03:57:36  brouard
 double *agedc, **covar, idx;    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.141  2014/01/26 02:42:01  brouard
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.140  2011/09/02 10:37:54  brouard
 {    Summary: times.h is ok with mingw32 now.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
    l1 = strlen( path );                 /* length of path */    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.138  2010/04/30 18:19:40  brouard
    s = strrchr( path, '\\' );           /* find last / */    *** empty log message ***
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.137  2010/04/29 18:11:38  brouard
 #endif    (Module): Checking covariates for more complex models
    if ( s == NULL ) {                   /* no directory, so use current */    than V1+V2. A lot of change to be done. Unstable.
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.136  2010/04/26 20:30:53  brouard
     (Module): merging some libgsl code. Fixing computation
       if ( getwd( dirc ) == NULL ) {    of likelione (using inter/intrapolation if mle = 0) in order to
 #else    get same likelihood as if mle=1.
       extern char       *getcwd( );    Some cleaning of code and comments added.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.135  2009/10/29 15:33:14  brouard
 #endif    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.134  2009/10/29 13:18:53  brouard
       strcpy( name, path );             /* we've got it */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.133  2009/07/06 10:21:25  brouard
       l2 = strlen( s );                 /* length of filename */    just nforces
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.132  2009/07/06 08:22:05  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Many tings
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.131  2009/06/20 16:22:47  brouard
    l1 = strlen( dirc );                 /* length of directory */    Some dimensions resccaled
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.130  2009/05/26 06:44:34  brouard
 #else    (Module): Max Covariate is now set to 20 instead of 8. A
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    lot of cleaning with variables initialized to 0. Trying to make
 #endif    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.129  2007/08/31 13:49:27  lievre
    strcpy(ext,s);                       /* save extension */    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.128  2006/06/30 13:02:05  brouard
    strncpy( finame, name, l1-l2);    (Module): Clarifications on computing e.j
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.127  2006/04/28 18:11:50  brouard
 }    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 /******************************************/    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
 void replace(char *s, char*t)    and then all the health expectancies with variances or standard
 {    deviation (needs data from the Hessian matrices) which slows the
   int i;    computation.
   int lg=20;    In the future we should be able to stop the program is only health
   i=0;    expectancies and graph are needed without standard deviations.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.126  2006/04/28 17:23:28  brouard
     (s[i] = t[i]);    (Module): Yes the sum of survivors was wrong since
     if (t[i]== '\\') s[i]='/';    imach-114 because nhstepm was no more computed in the age
   }    loop. Now we define nhstepma in the age loop.
 }    Version 0.98h
   
 int nbocc(char *s, char occ)    Revision 1.125  2006/04/04 15:20:31  lievre
 {    Errors in calculation of health expectancies. Age was not initialized.
   int i,j=0;    Forecasting file added.
   int lg=20;  
   i=0;    Revision 1.124  2006/03/22 17:13:53  lievre
   lg=strlen(s);    Parameters are printed with %lf instead of %f (more numbers after the comma).
   for(i=0; i<= lg; i++) {    The log-likelihood is printed in the log file
   if  (s[i] == occ ) j++;  
   }    Revision 1.123  2006/03/20 10:52:43  brouard
   return j;    * imach.c (Module): <title> changed, corresponds to .htm file
 }    name. <head> headers where missing.
   
 void cutv(char *u,char *v, char*t, char occ)    * imach.c (Module): Weights can have a decimal point as for
 {    English (a comma might work with a correct LC_NUMERIC environment,
   int i,lg,j,p=0;    otherwise the weight is truncated).
   i=0;    Modification of warning when the covariates values are not 0 or
   for(j=0; j<=strlen(t)-1; j++) {    1.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Version 0.98g
   }  
     Revision 1.122  2006/03/20 09:45:41  brouard
   lg=strlen(t);    (Module): Weights can have a decimal point as for
   for(j=0; j<p; j++) {    English (a comma might work with a correct LC_NUMERIC environment,
     (u[j] = t[j]);    otherwise the weight is truncated).
   }    Modification of warning when the covariates values are not 0 or
      u[p]='\0';    1.
     Version 0.98g
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.121  2006/03/16 17:45:01  lievre
   }    * imach.c (Module): Comments concerning covariates added
 }  
     * imach.c (Module): refinements in the computation of lli if
 /********************** nrerror ********************/    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 void nrerror(char error_text[])  
 {    Revision 1.120  2006/03/16 15:10:38  lievre
   fprintf(stderr,"ERREUR ...\n");    (Module): refinements in the computation of lli if
   fprintf(stderr,"%s\n",error_text);    status=-2 in order to have more reliable computation if stepm is
   exit(1);    not 1 month. Version 0.98f
 }  
 /*********************** vector *******************/    Revision 1.119  2006/03/15 17:42:26  brouard
 double *vector(int nl, int nh)    (Module): Bug if status = -2, the loglikelihood was
 {    computed as likelihood omitting the logarithm. Version O.98e
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.118  2006/03/14 18:20:07  brouard
   if (!v) nrerror("allocation failure in vector");    (Module): varevsij Comments added explaining the second
   return v-nl+NR_END;    table of variances if popbased=1 .
 }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 /************************ free vector ******************/    (Module): Version 0.98d
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.117  2006/03/14 17:16:22  brouard
   free((FREE_ARG)(v+nl-NR_END));    (Module): varevsij Comments added explaining the second
 }    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /************************ivector *******************************/    (Module): Function pstamp added
 int *ivector(long nl,long nh)    (Module): Version 0.98d
 {  
   int *v;    Revision 1.116  2006/03/06 10:29:27  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): Variance-covariance wrong links and
   if (!v) nrerror("allocation failure in ivector");    varian-covariance of ej. is needed (Saito).
   return v-nl+NR_END;  
 }    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.114  2006/02/26 12:57:58  brouard
 {    (Module): Some improvements in processing parameter
   free((FREE_ARG)(v+nl-NR_END));    filename with strsep.
 }  
     Revision 1.113  2006/02/24 14:20:24  brouard
 /******************* imatrix *******************************/    (Module): Memory leaks checks with valgrind and:
 int **imatrix(long nrl, long nrh, long ncl, long nch)    datafile was not closed, some imatrix were not freed and on matrix
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    allocation too.
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.112  2006/01/30 09:55:26  brouard
   int **m;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    
   /* allocate pointers to rows */    Revision 1.111  2006/01/25 20:38:18  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Module): Lots of cleaning and bugs added (Gompertz)
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Comments can be added in data file. Missing date values
   m += NR_END;    can be a simple dot '.'.
   m -= nrl;  
      Revision 1.110  2006/01/25 00:51:50  brouard
      (Module): Lots of cleaning and bugs added (Gompertz)
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.109  2006/01/24 19:37:15  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Comments (lines starting with a #) are allowed in data.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.108  2006/01/19 18:05:42  lievre
      Gnuplot problem appeared...
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    To be fixed
    
   /* return pointer to array of pointers to rows */    Revision 1.107  2006/01/19 16:20:37  brouard
   return m;    Test existence of gnuplot in imach path
 }  
     Revision 1.106  2006/01/19 13:24:36  brouard
 /****************** free_imatrix *************************/    Some cleaning and links added in html output
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.105  2006/01/05 20:23:19  lievre
       long nch,ncl,nrh,nrl;    *** empty log message ***
      /* free an int matrix allocated by imatrix() */  
 {    Revision 1.104  2005/09/30 16:11:43  lievre
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    (Module): sump fixed, loop imx fixed, and simplifications.
   free((FREE_ARG) (m+nrl-NR_END));    (Module): If the status is missing at the last wave but we know
 }    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
 /******************* matrix *******************************/    contributions to the likelihood is 1 - Prob of dying from last
 double **matrix(long nrl, long nrh, long ncl, long nch)    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 {    the healthy state at last known wave). Version is 0.98
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.102  2004/09/15 17:31:30  brouard
   m += NR_END;    Add the possibility to read data file including tab characters.
   m -= nrl;  
     Revision 1.101  2004/09/15 10:38:38  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Fix on curr_time
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.100  2004/07/12 18:29:06  brouard
   m[nrl] -= ncl;    Add version for Mac OS X. Just define UNIX in Makefile
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.99  2004/06/05 08:57:40  brouard
   return m;    *** empty log message ***
 }  
     Revision 1.98  2004/05/16 15:05:56  brouard
 /*************************free matrix ************************/    New version 0.97 . First attempt to estimate force of mortality
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    directly from the data i.e. without the need of knowing the health
 {    state at each age, but using a Gompertz model: log u =a + b*age .
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    This is the basic analysis of mortality and should be done before any
   free((FREE_ARG)(m+nrl-NR_END));    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.
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    The same imach parameter file can be used but the option for mle should be -3.
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Agnès, who wrote this part of the code, tried to keep most of the
   double ***m;    former routines in order to include the new code within the former code.
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    The output is very simple: only an estimate of the intercept and of
   if (!m) nrerror("allocation failure 1 in matrix()");    the slope with 95% confident intervals.
   m += NR_END;  
   m -= nrl;    Current limitations:
     A) Even if you enter covariates, i.e. with the
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    B) There is no computation of Life Expectancy nor Life Table.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    suppressed.
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Revision 1.96  2003/07/15 15:38:55  brouard
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   m[nrl][ncl] += NR_END;    rewritten within the same printf. Workaround: many printfs.
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.95  2003/07/08 07:54:34  brouard
     m[nrl][j]=m[nrl][j-1]+nlay;    * imach.c (Repository):
      (Repository): Using imachwizard code to output a more meaningful covariance
   for (i=nrl+1; i<=nrh; i++) {    matrix (cov(a12,c31) instead of numbers.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.94  2003/06/27 13:00:02  brouard
       m[i][j]=m[i][j-1]+nlay;    Just cleaning
   }  
   return m;    Revision 1.93  2003/06/25 16:33:55  brouard
 }    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 /*************************free ma3x ************************/    (Module): Version 0.96b
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    Revision 1.92  2003/06/25 16:30:45  brouard
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    (Module): On windows (cygwin) function asctime_r doesn't
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    exist so I changed back to asctime which exists.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
 /***************** f1dim *************************/    (Repository): Elapsed time after each iteration is now output. It
 extern int ncom;    helps to forecast when convergence will be reached. Elapsed time
 extern double *pcom,*xicom;    is stamped in powell.  We created a new html file for the graphs
 extern double (*nrfunc)(double []);    concerning matrix of covariance. It has extension -cov.htm.
    
 double f1dim(double x)    Revision 1.90  2003/06/24 12:34:15  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   int j;    mle=-1 a template is output in file "or"mypar.txt with the design
   double f;    of the covariance matrix to be input.
   double *xt;  
      Revision 1.89  2003/06/24 12:30:52  brouard
   xt=vector(1,ncom);    (Module): Some bugs corrected for windows. Also, when
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    mle=-1 a template is output in file "or"mypar.txt with the design
   f=(*nrfunc)(xt);    of the covariance matrix to be input.
   free_vector(xt,1,ncom);  
   return f;    Revision 1.88  2003/06/23 17:54:56  brouard
 }    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   
 /*****************brent *************************/    Revision 1.87  2003/06/18 12:26:01  brouard
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Version 0.96
 {  
   int iter;    Revision 1.86  2003/06/17 20:04:08  brouard
   double a,b,d,etemp;    (Module): Change position of html and gnuplot routines and added
   double fu,fv,fw,fx;    routine fileappend.
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    Revision 1.85  2003/06/17 13:12:43  brouard
   double e=0.0;    * imach.c (Repository): Check when date of death was earlier that
      current date of interview. It may happen when the death was just
   a=(ax < cx ? ax : cx);    prior to the death. In this case, dh was negative and likelihood
   b=(ax > cx ? ax : cx);    was wrong (infinity). We still send an "Error" but patch by
   x=w=v=bx;    assuming that the date of death was just one stepm after the
   fw=fv=fx=(*f)(x);    interview.
   for (iter=1;iter<=ITMAX;iter++) {    (Repository): Because some people have very long ID (first column)
     xm=0.5*(a+b);    we changed int to long in num[] and we added a new lvector for
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    memory allocation. But we also truncated to 8 characters (left
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    truncation)
     printf(".");fflush(stdout);    (Repository): No more line truncation errors.
 #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);    Revision 1.84  2003/06/13 21:44:43  brouard
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    * imach.c (Repository): Replace "freqsummary" at a correct
 #endif    place. It differs from routine "prevalence" which may be called
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    many times. Probs is memory consuming and must be used with
       *xmin=x;    parcimony.
       return fx;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
     }  
     ftemp=fu;    Revision 1.83  2003/06/10 13:39:11  lievre
     if (fabs(e) > tol1) {    *** empty log message ***
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    Revision 1.82  2003/06/05 15:57:20  brouard
       p=(x-v)*q-(x-w)*r;    Add log in  imach.c and  fullversion number is now printed.
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  */
       q=fabs(q);  /*
       etemp=e;     Interpolated Markov Chain
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    Short summary of the programme:
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    
       else {    This program computes Healthy Life Expectancies from
         d=p/q;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
         u=x+d;    first survey ("cross") where individuals from different ages are
         if (u-a < tol2 || b-u < tol2)    interviewed on their health status or degree of disability (in the
           d=SIGN(tol1,xm-x);    case of a health survey which is our main interest) -2- at least a
       }    second wave of interviews ("longitudinal") which measure each change
     } else {    (if any) in individual health status.  Health expectancies are
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    computed from the time spent in each health state according to a
     }    model. More health states you consider, more time is necessary to reach the
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    Maximum Likelihood of the parameters involved in the model.  The
     fu=(*f)(u);    simplest model is the multinomial logistic model where pij is the
     if (fu <= fx) {    probability to be observed in state j at the second wave
       if (u >= x) a=x; else b=x;    conditional to be observed in state i at the first wave. Therefore
       SHFT(v,w,x,u)    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
         SHFT(fv,fw,fx,fu)    'age' is age and 'sex' is a covariate. If you want to have a more
         } else {    complex model than "constant and age", you should modify the program
           if (u < x) a=u; else b=u;    where the markup *Covariates have to be included here again* invites
           if (fu <= fw || w == x) {    you to do it.  More covariates you add, slower the
             v=w;    convergence.
             w=u;  
             fv=fw;    The advantage of this computer programme, compared to a simple
             fw=fu;    multinomial logistic model, is clear when the delay between waves is not
           } else if (fu <= fv || v == x || v == w) {    identical for each individual. Also, if a individual missed an
             v=u;    intermediate interview, the information is lost, but taken into
             fv=fu;    account using an interpolation or extrapolation.  
           }  
         }    hPijx is the probability to be observed in state i at age x+h
   }    conditional to the observed state i at age x. The delay 'h' can be
   nrerror("Too many iterations in brent");    split into an exact number (nh*stepm) of unobserved intermediate
   *xmin=x;    states. This elementary transition (by month, quarter,
   return fx;    semester or year) is modelled as a multinomial logistic.  The hPx
 }    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 /****************** mnbrak ***********************/    hPijx.
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Also this programme outputs the covariance matrix of the parameters but also
             double (*func)(double))    of the life expectancies. It also computes the period (stable) prevalence. 
 {    
   double ulim,u,r,q, dum;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   double fu;             Institut national d'études démographiques, Paris.
      This software have been partly granted by Euro-REVES, a concerted action
   *fa=(*func)(*ax);    from the European Union.
   *fb=(*func)(*bx);    It is copyrighted identically to a GNU software product, ie programme and
   if (*fb > *fa) {    software can be distributed freely for non commercial use. Latest version
     SHFT(dum,*ax,*bx,dum)    can be accessed at http://euroreves.ined.fr/imach .
       SHFT(dum,*fb,*fa,dum)  
       }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   *cx=(*bx)+GOLD*(*bx-*ax);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   *fc=(*func)(*cx);    
   while (*fb > *fc) {    **********************************************************************/
     r=(*bx-*ax)*(*fb-*fc);  /*
     q=(*bx-*cx)*(*fb-*fa);    main
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    read parameterfile
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    read datafile
     ulim=(*bx)+GLIMIT*(*cx-*bx);    concatwav
     if ((*bx-u)*(u-*cx) > 0.0) {    freqsummary
       fu=(*func)(u);    if (mle >= 1)
     } else if ((*cx-u)*(u-ulim) > 0.0) {      mlikeli
       fu=(*func)(u);    print results files
       if (fu < *fc) {    if mle==1 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))       computes hessian
           SHFT(*fb,*fc,fu,(*func)(u))    read end of parameter file: agemin, agemax, bage, fage, estepm
           }        begin-prev-date,...
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    open gnuplot file
       u=ulim;    open html file
       fu=(*func)(u);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
     } else {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
       u=(*cx)+GOLD*(*cx-*bx);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       fu=(*func)(u);      freexexit2 possible for memory heap.
     }  
     SHFT(*ax,*bx,*cx,u)    h Pij x                         | pij_nom  ficrestpij
       SHFT(*fa,*fb,*fc,fu)     # 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
 }         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   
 /*************** linmin ************************/         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
          1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
 int ncom;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
 double *pcom,*xicom;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
 double (*nrfunc)(double []);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    forecasting if prevfcast==1 prevforecast call prevalence()
 {    health expectancies
   double brent(double ax, double bx, double cx,    Variance-covariance of DFLE
                double (*f)(double), double tol, double *xmin);    prevalence()
   double f1dim(double x);     movingaverage()
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    varevsij() 
               double *fc, double (*func)(double));    if popbased==1 varevsij(,popbased)
   int j;    total life expectancies
   double xx,xmin,bx,ax;    Variance of period (stable) prevalence
   double fx,fb,fa;   end
    */
   ncom=n;  
   pcom=vector(1,n);  #define POWELL /* Instead of NLOPT */
   xicom=vector(1,n);  
   nrfunc=func;  #include <math.h>
   for (j=1;j<=n;j++) {  #include <stdio.h>
     pcom[j]=p[j];  #include <stdlib.h>
     xicom[j]=xi[j];  #include <string.h>
   }  
   ax=0.0;  #ifdef _WIN32
   xx=1.0;  #include <io.h>
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #include <windows.h>
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #include <tchar.h>
 #ifdef DEBUG  #else
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #include <unistd.h>
 #endif  #endif
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  #include <limits.h>
     p[j] += xi[j];  #include <sys/types.h>
   }  
   free_vector(xicom,1,n);  #if defined(__GNUC__)
   free_vector(pcom,1,n);  #include <sys/utsname.h> /* Doesn't work on Windows */
 }  #endif
   
 /*************** powell ************************/  #include <sys/stat.h>
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #include <errno.h>
             double (*func)(double []))  /* extern int errno; */
 {  
   void linmin(double p[], double xi[], int n, double *fret,  /* #ifdef LINUX */
               double (*func)(double []));  /* #include <time.h> */
   int i,ibig,j;  /* #include "timeval.h" */
   double del,t,*pt,*ptt,*xit;  /* #else */
   double fp,fptt;  /* #include <sys/time.h> */
   double *xits;  /* #endif */
   pt=vector(1,n);  
   ptt=vector(1,n);  #include <time.h>
   xit=vector(1,n);  
   xits=vector(1,n);  #ifdef GSL
   *fret=(*func)(p);  #include <gsl/gsl_errno.h>
   for (j=1;j<=n;j++) pt[j]=p[j];  #include <gsl/gsl_multimin.h>
   for (*iter=1;;++(*iter)) {  #endif
     fp=(*fret);  
     ibig=0;  
     del=0.0;  #ifdef NLOPT
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #include <nlopt.h>
     for (i=1;i<=n;i++)  typedef struct {
       printf(" %d %.12f",i, p[i]);    double (* function)(double [] );
     printf("\n");  } myfunc_data ;
     for (i=1;i<=n;i++) {  #endif
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /* #include <libintl.h> */
 #ifdef DEBUG  /* #define _(String) gettext (String) */
       printf("fret=%lf \n",*fret);  
 #endif  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  #define GNUPLOTPROGRAM "gnuplot"
       if (fabs(fptt-(*fret)) > del) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         del=fabs(fptt-(*fret));  #define FILENAMELENGTH 132
         ibig=i;  
       }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #ifdef DEBUG  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  #define NINTERVMAX 8
       for(j=1;j<=n;j++)  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
         printf(" p=%.12e",p[j]);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       printf("\n");  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 #endif  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
     }  #define MAXN 20000
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define YEARM 12. /**< Number of months per year */
 #ifdef DEBUG  #define AGESUP 130
       int k[2],l;  #define AGEBASE 40
       k[0]=1;  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
       k[1]=-1;  #ifdef _WIN32
       printf("Max: %.12e",(*func)(p));  #define DIRSEPARATOR '\\'
       for (j=1;j<=n;j++)  #define CHARSEPARATOR "\\"
         printf(" %.12e",p[j]);  #define ODIRSEPARATOR '/'
       printf("\n");  #else
       for(l=0;l<=1;l++) {  #define DIRSEPARATOR '/'
         for (j=1;j<=n;j++) {  #define CHARSEPARATOR "/"
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #define ODIRSEPARATOR '\\'
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #endif
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /* $Id$ */
       }  /* $State$ */
 #endif  
   char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
   char fullversion[]="$Revision$ $Date$"; 
       free_vector(xit,1,n);  char strstart[80];
       free_vector(xits,1,n);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       free_vector(ptt,1,n);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       free_vector(pt,1,n);  int nvar=0, nforce=0; /* Number of variables, number of forces */
       return;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
     }  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     for (j=1;j<=n;j++) {  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       ptt[j]=2.0*p[j]-pt[j];  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       xit[j]=p[j]-pt[j];  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       pt[j]=p[j];  int cptcoveff=0; /* Total number of covariates to vary for printing results */
     }  int cptcov=0; /* Working variable */
     fptt=(*func)(ptt);  int npar=NPARMAX;
     if (fptt < fp) {  int nlstate=2; /* Number of live states */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  int ndeath=1; /* Number of dead states */
       if (t < 0.0) {  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
         linmin(p,xit,n,fret,func);  int popbased=0;
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  int *wav; /* Number of waves for this individuual 0 is possible */
           xi[j][n]=xit[j];  int maxwav=0; /* Maxim number of waves */
         }  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 #ifdef DEBUG  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
         for(j=1;j<=n;j++)                     to the likelihood and the sum of weights (done by funcone)*/
           printf(" %.12e",xit[j]);  int mle=1, weightopt=0;
         printf("\n");  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #endif  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   }  int countcallfunc=0;  /* Count the number of calls to func */
 }  double jmean=1; /* Mean space between 2 waves */
   double **matprod2(); /* test */
 /**** Prevalence limit ****************/  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /*FILE *fic ; */ /* Used in readdata only */
 {  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  FILE *ficlog, *ficrespow;
      matrix by transitions matrix until convergence is reached */  int globpr=0; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
   int i, ii,j,k;  long ipmx=0; /* Number of contributions */
   double min, max, maxmin, maxmax,sumnew=0.;  double sw; /* Sum of weights */
   double **matprod2();  char filerespow[FILENAMELENGTH];
   double **out, cov[NCOVMAX], **pmij();  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double **newm;  FILE *ficresilk;
   double agefin, delaymax=50 ; /* Max number of years to converge */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
   for (ii=1;ii<=nlstate+ndeath;ii++)  FILE *fichtm, *fichtmcov; /* Html File */
     for (j=1;j<=nlstate+ndeath;j++){  FILE *ficreseij;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char filerese[FILENAMELENGTH];
     }  FILE *ficresstdeij;
   char fileresstde[FILENAMELENGTH];
    cov[1]=1.;  FILE *ficrescveij;
    char filerescve[FILENAMELENGTH];
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  FILE  *ficresvij;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  char fileresv[FILENAMELENGTH];
     newm=savm;  FILE  *ficresvpl;
     /* Covariates have to be included here again */  char fileresvpl[FILENAMELENGTH];
      cov[2]=agefin;  char title[MAXLINE];
    char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       for (k=1; k<=cptcovn;k++) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  char command[FILENAMELENGTH];
       }  int  outcmd=0;
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       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]]];  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  char fileregp[FILENAMELENGTH];
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  char popfile[FILENAMELENGTH];
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
     savm=oldm;  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
     oldm=newm;  /* struct timezone tzp; */
     maxmax=0.;  /* extern int gettimeofday(); */
     for(j=1;j<=nlstate;j++){  struct tm tml, *gmtime(), *localtime();
       min=1.;  
       max=0.;  extern time_t time();
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  struct tm start_time, end_time, curr_time, last_time, forecast_time;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
         prlim[i][j]= newm[i][j]/(1-sumnew);  struct tm tm;
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);  char strcurr[80], strfor[80];
       }  
       maxmin=max-min;  char *endptr;
       maxmax=FMAX(maxmax,maxmin);  long lval;
     }  double dval;
     if(maxmax < ftolpl){  
       return prlim;  #define NR_END 1
     }  #define FREE_ARG char*
   }  #define FTOL 1.0e-10
 }  
   #define NRANSI 
 /*************** transition probabilities ***************/  #define ITMAX 200 
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #define TOL 2.0e-4 
 {  
   double s1, s2;  #define CGOLD 0.3819660 
   /*double t34;*/  #define ZEPS 1.0e-10 
   int i,j,j1, nc, ii, jj;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
     for(i=1; i<= nlstate; i++){  #define GOLD 1.618034 
     for(j=1; j<i;j++){  #define GLIMIT 100.0 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define TINY 1.0e-20 
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  static double maxarg1,maxarg2;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       ps[i][j]=s2;    
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     }  #define rint(a) floor(a+0.5)
     for(j=i+1; j<=nlstate+ndeath;j++){  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /* #define mytinydouble 1.0e-16 */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
       }  /* static double dsqrarg; */
       ps[i][j]=s2;  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
     }  static double sqrarg;
   }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     /*ps[3][2]=1;*/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
   for(i=1; i<= nlstate; i++){  
      s1=0;  int imx; 
     for(j=1; j<i; j++)  int stepm=1;
       s1+=exp(ps[i][j]);  /* Stepm, step in month: minimum step interpolation*/
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  int estepm;
     ps[i][i]=1./(s1+1.);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  int m,nb;
     for(j=i+1; j<=nlstate+ndeath; j++)  long *num;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   } /* end i */  double **pmmij, ***probs;
   double *ageexmed,*agecens;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  double dateintmean=0;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  double *weight;
       ps[ii][ii]=1;  int **s; /* Status */
     }  double *agedc;
   }  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                     * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  double  idx; 
     for(jj=1; jj<= nlstate+ndeath; jj++){  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
      printf("%lf ",ps[ii][jj]);  int *Ndum; /** Freq of modality (tricode */
    }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
     printf("\n ");  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     }  double *lsurv, *lpop, *tpop;
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  double ftolhess; /**< Tolerance for computing hessian */
   goto end;*/  
     return ps;  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 /**************** Product of 2 matrices ******************/    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    */ 
 {    char  *ss;                            /* pointer */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    int   l1, l2;                         /* length counters */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized    l1 = strlen(path );                   /* length of path */
      before: only the contents of out is modified. The function returns    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
      a pointer to pointers identical to out */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   long i, j, k;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   for(i=nrl; i<= nrh; i++)      strcpy( name, path );               /* we got the fullname name because no directory */
     for(k=ncolol; k<=ncoloh; k++)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         out[i][k] +=in[i][j]*b[j][k];      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
   return out;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 }        return( GLOCK_ERROR_GETCWD );
       }
       /* got dirc from getcwd*/
 /************* Higher Matrix Product ***************/      printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
      duration (i.e. until      strcpy( name, ss );         /* save file name */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      dirc[l1-l2] = 0;                    /* add zero */
      (typically every 2 years instead of every month which is too big).      printf(" DIRC2 = %s \n",dirc);
      Model is determined by parameters x and covariates have to be    }
      included manually here.    /* We add a separator at the end of dirc if not exists */
     l1 = strlen( dirc );                  /* length of directory */
      */    if( dirc[l1-1] != DIRSEPARATOR ){
       dirc[l1] =  DIRSEPARATOR;
   int i, j, d, h, k;      dirc[l1+1] = 0; 
   double **out, cov[NCOVMAX];      printf(" DIRC3 = %s \n",dirc);
   double **newm;    }
     ss = strrchr( name, '.' );            /* find last / */
   /* Hstepm could be zero and should return the unit matrix */    if (ss >0){
   for (i=1;i<=nlstate+ndeath;i++)      ss++;
     for (j=1;j<=nlstate+ndeath;j++){      strcpy(ext,ss);                     /* save extension */
       oldm[i][j]=(i==j ? 1.0 : 0.0);      l1= strlen( name);
       po[i][j][0]=(i==j ? 1.0 : 0.0);      l2= strlen(ss)+1;
     }      strncpy( finame, name, l1-l2);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      finame[l1-l2]= 0;
   for(h=1; h <=nhstepm; h++){    }
     for(d=1; d <=hstepm; d++){  
       newm=savm;    return( 0 );                          /* we're done */
       /* 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++) 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];  void replace_back_to_slash(char *s, char*t)
       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]]];    int i;
     int lg=0;
     i=0;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    lg=strlen(t);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    for(i=0; i<= lg; i++) {
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      (s[i] = t[i]);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      if (t[i]== '\\') s[i]='/';
       savm=oldm;    }
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  char *trimbb(char *out, char *in)
       for(j=1;j<=nlstate+ndeath;j++) {  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
         po[i][j][h]=newm[i][j];    char *s;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    s=out;
          */    while (*in != '\0'){
       }      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   } /* end h */        in++;
   return po;      }
 }      *out++ = *in++;
     }
     *out='\0';
 /*************** log-likelihood *************/    return s;
 double func( double *x)  }
 {  
   int i, ii, j, k, mi, d, kk;  char *cutl(char *blocc, char *alocc, char *in, char occ)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  {
   double **out;    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
   double sw; /* Sum of weights */       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   double lli; /* Individual log likelihood */       gives blocc="abcdef2ghi" and alocc="j".
   long ipmx;       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   /*extern weight */    */
   /* We are differentiating ll according to initial status */    char *s, *t;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    t=in;s=in;
   /*for(i=1;i<imx;i++)    while ((*in != occ) && (*in != '\0')){
     printf(" %d\n",s[4][i]);      *alocc++ = *in++;
   */    }
   cov[1]=1.;    if( *in == occ){
       *(alocc)='\0';
   for(k=1; k<=nlstate; k++) ll[k]=0.;      s=++in;
   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++){    if (s == t) {/* occ not found */
       for (ii=1;ii<=nlstate+ndeath;ii++)      *(alocc-(in-s))='\0';
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      in=s;
       for(d=0; d<dh[mi][i]; d++){    }
         newm=savm;    while ( *in != '\0'){
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      *blocc++ = *in++;
         for (kk=1; kk<=cptcovage;kk++) {    }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }    *blocc='\0';
            return t;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  char *cutv(char *blocc, char *alocc, char *in, char occ)
         savm=oldm;  {
         oldm=newm;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
               and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
               gives blocc="abcdef2ghi" and alocc="j".
       } /* end mult */       If occ is not found blocc is null and alocc is equal to in. Returns alocc
          */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    char *s, *t;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    t=in;s=in;
       ipmx +=1;    while (*in != '\0'){
       sw += weight[i];      while( *in == occ){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        *blocc++ = *in++;
     } /* end of wave */        s=in;
   } /* end of individual */      }
       *blocc++ = *in++;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    if (s == t) /* occ not found */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      *(blocc-(in-s))='\0';
   return -l;    else
 }      *(blocc-(in-s)-1)='\0';
     in=s;
     while ( *in != '\0'){
 /*********** Maximum Likelihood Estimation ***************/      *alocc++ = *in++;
     }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {    *alocc='\0';
   int i,j, iter;    return s;
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  int nbocc(char *s, char occ)
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++)    int i,j=0;
       xi[i][j]=(i==j ? 1.0 : 0.0);    int lg=20;
   printf("Powell\n");    i=0;
   powell(p,xi,npar,ftol,&iter,&fret,func);    lg=strlen(s);
     for(i=0; i<= lg; i++) {
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    if  (s[i] == occ ) j++;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    }
     return j;
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  /* void cutv(char *u,char *v, char*t, char occ) */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /* { */
 {  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   double  **a,**y,*x,pd;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   double **hess;  /*      gives u="abcdef2ghi" and v="j" *\/ */
   int i, j,jk;  /*   int i,lg,j,p=0; */
   int *indx;  /*   i=0; */
   /*   lg=strlen(t); */
   double hessii(double p[], double delta, int theta, double delti[]);  /*   for(j=0; j<=lg-1; j++) { */
   double hessij(double p[], double delti[], int i, int j);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  /*   } */
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   /*   for(j=0; j<p; j++) { */
   hess=matrix(1,npar,1,npar);  /*     (u[j] = t[j]); */
   /*   } */
   printf("\nCalculation of the hessian matrix. Wait...\n");  /*      u[p]='\0'; */
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);  /*    for(j=0; j<= lg; j++) { */
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     /*printf(" %f ",p[i]);*/  /*   } */
     /*printf(" %lf ",hess[i][i]);*/  /* } */
   }  
    #ifdef _WIN32
   for (i=1;i<=npar;i++) {  char * strsep(char **pp, const char *delim)
     for (j=1;j<=npar;j++)  {  {
       if (j>i) {    char *p, *q;
         printf(".%d%d",i,j);fflush(stdout);           
         hess[i][j]=hessij(p,delti,i,j);    if ((p = *pp) == NULL)
         hess[j][i]=hess[i][j];          return 0;
         /*printf(" %lf ",hess[i][j]);*/    if ((q = strpbrk (p, delim)) != NULL)
       }    {
     }      *pp = q + 1;
   }      *q = '\0';
   printf("\n");    }
     else
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      *pp = 0;
      return p;
   a=matrix(1,npar,1,npar);  }
   y=matrix(1,npar,1,npar);  #endif
   x=vector(1,npar);  
   indx=ivector(1,npar);  /********************** nrerror ********************/
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  void nrerror(char error_text[])
   ludcmp(a,npar,indx,&pd);  {
     fprintf(stderr,"ERREUR ...\n");
   for (j=1;j<=npar;j++) {    fprintf(stderr,"%s\n",error_text);
     for (i=1;i<=npar;i++) x[i]=0;    exit(EXIT_FAILURE);
     x[j]=1;  }
     lubksb(a,npar,indx,x);  /*********************** vector *******************/
     for (i=1;i<=npar;i++){  double *vector(int nl, int nh)
       matcov[i][j]=x[i];  {
     }    double *v;
   }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
   printf("\n#Hessian matrix#\n");    return v-nl+NR_END;
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  /************************ free vector ******************/
     }  void free_vector(double*v, int nl, int nh)
     printf("\n");  {
   }    free((FREE_ARG)(v+nl-NR_END));
   }
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  /************************ivector *******************************/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  int *ivector(long nl,long nh)
   ludcmp(a,npar,indx,&pd);  {
     int *v;
   /*  printf("\n#Hessian matrix recomputed#\n");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
   for (j=1;j<=npar;j++) {    return v-nl+NR_END;
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  /******************free ivector **************************/
     for (i=1;i<=npar;i++){  void free_ivector(int *v, long nl, long nh)
       y[i][j]=x[i];  {
       printf("%.3e ",y[i][j]);    free((FREE_ARG)(v+nl-NR_END));
     }  }
     printf("\n");  
   }  /************************lvector *******************************/
   */  long *lvector(long nl,long nh)
   {
   free_matrix(a,1,npar,1,npar);    long *v;
   free_matrix(y,1,npar,1,npar);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   free_vector(x,1,npar);    if (!v) nrerror("allocation failure in ivector");
   free_ivector(indx,1,npar);    return v-nl+NR_END;
   free_matrix(hess,1,npar,1,npar);  }
   
   /******************free lvector **************************/
 }  void free_lvector(long *v, long nl, long nh)
   {
 /*************** hessian matrix ****************/    free((FREE_ARG)(v+nl-NR_END));
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /******************* imatrix *******************************/
   int l=1, lmax=20;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double k1,k2;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   double p2[NPARMAX+1];  { 
   double res;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    int **m; 
   double fx;    
   int k=0,kmax=10;    /* allocate pointers to rows */ 
   double l1;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
   fx=func(x);    m += NR_END; 
   for (i=1;i<=npar;i++) p2[i]=x[i];    m -= nrl; 
   for(l=0 ; l <=lmax; l++){    
     l1=pow(10,l);    
     delts=delt;    /* allocate rows and set pointers to them */ 
     for(k=1 ; k <kmax; k=k+1){    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       delt = delta*(l1*k);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       p2[theta]=x[theta] +delt;    m[nrl] += NR_END; 
       k1=func(p2)-fx;    m[nrl] -= ncl; 
       p2[theta]=x[theta]-delt;    
       k2=func(p2)-fx;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    /* return pointer to array of pointers to rows */ 
          return m; 
 #ifdef DEBUG  } 
       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);  
 #endif  /****************** free_imatrix *************************/
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  void free_imatrix(m,nrl,nrh,ncl,nch)
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        int **m;
         k=kmax;        long nch,ncl,nrh,nrl; 
       }       /* free an int matrix allocated by imatrix() */ 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  { 
         k=kmax; l=lmax*10.;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       }    free((FREE_ARG) (m+nrl-NR_END)); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  } 
         delts=delt;  
       }  /******************* matrix *******************************/
     }  double **matrix(long nrl, long nrh, long ncl, long nch)
   }  {
   delti[theta]=delts;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   return res;    double **m;
    
 }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 double hessij( double x[], double delti[], int thetai,int thetaj)    m += NR_END;
 {    m -= nrl;
   int i;  
   int l=1, l1, lmax=20;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double k1,k2,k3,k4,res,fx;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double p2[NPARMAX+1];    m[nrl] += NR_END;
   int k;    m[nrl] -= ncl;
   
   fx=func(x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (k=1; k<=2; k++) {    return m;
     for (i=1;i<=npar;i++) p2[i]=x[i];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     p2[thetai]=x[thetai]+delti[thetai]/k;  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     k1=func(p2)-fx;     */
    }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*************************free matrix ************************/
     k2=func(p2)-fx;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
    {
     p2[thetai]=x[thetai]-delti[thetai]/k;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    free((FREE_ARG)(m+nrl-NR_END));
     k3=func(p2)-fx;  }
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /******************* ma3x *******************************/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     k4=func(p2)-fx;  {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 #ifdef DEBUG    double ***m;
     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    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
   return res;    m += NR_END;
 }    m -= nrl;
   
 /************** Inverse of matrix **************/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 void ludcmp(double **a, int n, int *indx, double *d)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 {    m[nrl] += NR_END;
   int i,imax,j,k;    m[nrl] -= ncl;
   double big,dum,sum,temp;  
   double *vv;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    
   vv=vector(1,n);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   *d=1.0;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   for (i=1;i<=n;i++) {    m[nrl][ncl] += NR_END;
     big=0.0;    m[nrl][ncl] -= nll;
     for (j=1;j<=n;j++)    for (j=ncl+1; j<=nch; j++) 
       if ((temp=fabs(a[i][j])) > big) big=temp;      m[nrl][j]=m[nrl][j-1]+nlay;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    
     vv[i]=1.0/big;    for (i=nrl+1; i<=nrh; i++) {
   }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (j=1;j<=n;j++) {      for (j=ncl+1; j<=nch; j++) 
     for (i=1;i<j;i++) {        m[i][j]=m[i][j-1]+nlay;
       sum=a[i][j];    }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    return m; 
       a[i][j]=sum;    /*  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)
     big=0.0;    */
     for (i=j;i<=n;i++) {  }
       sum=a[i][j];  
       for (k=1;k<j;k++)  /*************************free ma3x ************************/
         sum -= a[i][k]*a[k][j];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       a[i][j]=sum;  {
       if ( (dum=vv[i]*fabs(sum)) >= big) {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         big=dum;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         imax=i;    free((FREE_ARG)(m+nrl-NR_END));
       }  }
     }  
     if (j != imax) {  /*************** function subdirf ***********/
       for (k=1;k<=n;k++) {  char *subdirf(char fileres[])
         dum=a[imax][k];  {
         a[imax][k]=a[j][k];    /* Caution optionfilefiname is hidden */
         a[j][k]=dum;    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/"); /* Add to the right */
       *d = -(*d);    strcat(tmpout,fileres);
       vv[imax]=vv[j];    return tmpout;
     }  }
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  /*************** function subdirf2 ***********/
     if (j != n) {  char *subdirf2(char fileres[], char *preop)
       dum=1.0/(a[j][j]);  {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    
     }    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
   free_vector(vv,1,n);  /* Doesn't work */    strcat(tmpout,"/");
 ;    strcat(tmpout,preop);
 }    strcat(tmpout,fileres);
     return tmpout;
 void lubksb(double **a, int n, int *indx, double b[])  }
 {  
   int i,ii=0,ip,j;  /*************** function subdirf3 ***********/
   double sum;  char *subdirf3(char fileres[], char *preop, char *preop2)
    {
   for (i=1;i<=n;i++) {    
     ip=indx[i];    /* Caution optionfilefiname is hidden */
     sum=b[ip];    strcpy(tmpout,optionfilefiname);
     b[ip]=b[i];    strcat(tmpout,"/");
     if (ii)    strcat(tmpout,preop);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    strcat(tmpout,preop2);
     else if (sum) ii=i;    strcat(tmpout,fileres);
     b[i]=sum;    return tmpout;
   }  }
   for (i=n;i>=1;i--) {  
     sum=b[i];  char *asc_diff_time(long time_sec, char ascdiff[])
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  {
     b[i]=sum/a[i][i];    long sec_left, days, hours, minutes;
   }    days = (time_sec) / (60*60*24);
 }    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
 /************ Frequencies ********************/    sec_left = (sec_left) %(60*60);
 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)    minutes = (sec_left) /60;
 {  /* Some frequencies */    sec_left = (sec_left) % (60);
      sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    return ascdiff;
   double ***freq; /* Frequencies */  }
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  /***************** f1dim *************************/
   FILE *ficresp;  extern int ncom; 
   char fileresp[FILENAMELENGTH];  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
   pp=vector(1,nlstate);   
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  double f1dim(double x) 
   strcpy(fileresp,"p");  { 
   strcat(fileresp,fileres);    int j; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double f;
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double *xt; 
     exit(0);   
   }    xt=vector(1,ncom); 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   j1=0;    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
   j=cptcoveff;    return f; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  } 
   
   for(k1=1; k1<=j;k1++){  /*****************brent *************************/
    for(i1=1; i1<=ncodemax[k1];i1++){  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
        j1++;  { 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    int iter; 
          scanf("%d", i);*/    double a,b,d,etemp;
         for (i=-1; i<=nlstate+ndeath; i++)      double fu=0,fv,fw,fx;
          for (jk=-1; jk<=nlstate+ndeath; jk++)      double ftemp=0.;
            for(m=agemin; m <= agemax+3; m++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
              freq[i][jk][m]=0;    double e=0.0; 
    
         dateintsum=0;    a=(ax < cx ? ax : cx); 
         k2cpt=0;    b=(ax > cx ? ax : cx); 
        for (i=1; i<=imx; i++) {    x=w=v=bx; 
          bool=1;    fw=fv=fx=(*f)(x); 
          if  (cptcovn>0) {    for (iter=1;iter<=ITMAX;iter++) { 
            for (z1=1; z1<=cptcoveff; z1++)      xm=0.5*(a+b); 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                bool=0;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
          }      printf(".");fflush(stdout);
          if (bool==1) {      fprintf(ficlog,".");fflush(ficlog);
            for(m=firstpass; m<=lastpass; m++){  #ifdef DEBUGBRENT
              k2=anint[m][i]+(mint[m][i]/12.);      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 ((k2>=dateprev1) && (k2<=dateprev2)) {      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
                if(agev[m][i]==0) agev[m][i]=agemax+1;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
                if(agev[m][i]==1) agev[m][i]=agemax+2;  #endif
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        *xmin=x; 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        return fx; 
                  dateintsum=dateintsum+k2;      } 
                  k2cpt++;      ftemp=fu;
                }      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
              }        q=(x-v)*(fx-fw); 
            }        p=(x-v)*q-(x-w)*r; 
          }        q=2.0*(q-r); 
        }        if (q > 0.0) p = -p; 
                q=fabs(q); 
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        etemp=e; 
         e=d; 
         if  (cptcovn>0) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
          fprintf(ficresp, "\n#********** Variable ");          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        else { 
        fprintf(ficresp, "**********\n#");          d=p/q; 
         }          u=x+d; 
        for(i=1; i<=nlstate;i++)          if (u-a < tol2 || b-u < tol2) 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            d=SIGN(tol1,xm-x); 
        fprintf(ficresp, "\n");        } 
              } else { 
   for(i=(int)agemin; i <= (int)agemax+3; i++){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     if(i==(int)agemax+3)      } 
       printf("Total");      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     else      fu=(*f)(u); 
       printf("Age %d", i);      if (fu <= fx) { 
     for(jk=1; jk <=nlstate ; jk++){        if (u >= x) a=x; else b=x; 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        SHFT(v,w,x,u) 
         pp[jk] += freq[jk][m][i];          SHFT(fv,fw,fx,fu) 
     }          } else { 
     for(jk=1; jk <=nlstate ; jk++){            if (u < x) a=u; else b=u; 
       for(m=-1, pos=0; m <=0 ; m++)            if (fu <= fw || w == x) { 
         pos += freq[jk][m][i];              v=w; 
       if(pp[jk]>=1.e-10)              w=u; 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              fv=fw; 
       else              fw=fu; 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
               fv=fu; 
      for(jk=1; jk <=nlstate ; jk++){            } 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          } 
         pp[jk] += freq[jk][m][i];    } 
      }    nrerror("Too many iterations in brent"); 
     *xmin=x; 
     for(jk=1,pos=0; jk <=nlstate ; jk++)    return fx; 
       pos += pp[jk];  } 
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)  /****************** mnbrak ***********************/
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
       else  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              double (*func)(double)) 
       if( i <= (int) agemax){  { 
         if(pos>=1.e-5){    double ulim,u,r,q, dum;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    double fu; 
           probs[i][jk][j1]= pp[jk]/pos;   
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    *fa=(*func)(*ax); 
         }    *fb=(*func)(*bx); 
       else    if (*fb > *fa) { 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      SHFT(dum,*ax,*bx,dum) 
       }        SHFT(dum,*fb,*fa,dum) 
     }        } 
     for(jk=-1; jk <=nlstate+ndeath; jk++)    *cx=(*bx)+GOLD*(*bx-*ax); 
       for(m=-1; m <=nlstate+ndeath; m++)    *fc=(*func)(*cx); 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    while (*fb > *fc) { /* Declining fa, fb, fc */
     if(i <= (int) agemax)      r=(*bx-*ax)*(*fb-*fc); 
       fprintf(ficresp,"\n");      q=(*bx-*cx)*(*fb-*fa); 
     printf("\n");      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
     }      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
  }      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
   dateintmean=dateintsum/k2cpt;        fu=(*func)(u); 
    #ifdef DEBUG
   fclose(ficresp);        /* f(x)=A(x-u)**2+f(u) */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        double A, fparabu; 
   free_vector(pp,1,nlstate);        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         fparabu= *fa - A*(*ax-u)*(*ax-u);
   /* End of Freq */        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
 }        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
   #endif 
 /************ Prevalence ********************/      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        fu=(*func)(u); 
 {  /* Some frequencies */        if (fu < *fc) { 
            SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double ***freq; /* Frequencies */            } 
   double *pp;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   double pos, k2;        u=ulim; 
         fu=(*func)(u); 
   pp=vector(1,nlstate);      } else { 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        u=(*cx)+GOLD*(*cx-*bx); 
          fu=(*func)(u); 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      } 
   j1=0;      SHFT(*ax,*bx,*cx,u) 
          SHFT(*fa,*fb,*fc,fu) 
   j=cptcoveff;        } 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  } 
    
  for(k1=1; k1<=j;k1++){  /*************** linmin ************************/
     for(i1=1; i1<=ncodemax[k1];i1++){  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
       j1++;  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
    and replaces xi by the actual vector displacement that p was moved. Also returns as fret
       for (i=-1; i<=nlstate+ndeath; i++)    the value of func at the returned location p . This is actually all accomplished by calling the
         for (jk=-1; jk<=nlstate+ndeath; jk++)    routines mnbrak and brent .*/
           for(m=agemin; m <= agemax+3; m++)  int ncom; 
             freq[i][jk][m]=0;  double *pcom,*xicom;
        double (*nrfunc)(double []); 
       for (i=1; i<=imx; i++) {   
         bool=1;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         if  (cptcovn>0) {  { 
           for (z1=1; z1<=cptcoveff; z1++)    double brent(double ax, double bx, double cx, 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])                 double (*f)(double), double tol, double *xmin); 
               bool=0;    double f1dim(double x); 
         }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         if (bool==1) {                double *fc, double (*func)(double)); 
           for(m=firstpass; m<=lastpass; m++){    int j; 
             k2=anint[m][i]+(mint[m][i]/12.);    double xx,xmin,bx,ax; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    double fx,fb,fa;
               if(agev[m][i]==0) agev[m][i]=agemax+1;   
               if(agev[m][i]==1) agev[m][i]=agemax+2;    ncom=n; 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    pcom=vector(1,n); 
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];      xicom=vector(1,n); 
             }    nrfunc=func; 
           }    for (j=1;j<=n;j++) { 
         }      pcom[j]=p[j]; 
       }      xicom[j]=xi[j]; 
          } 
         for(i=(int)agemin; i <= (int)agemax+3; i++){    ax=0.0; 
           for(jk=1; jk <=nlstate ; jk++){    xx=1.0; 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
               pp[jk] += freq[jk][m][i];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
           }  #ifdef DEBUG
           for(jk=1; jk <=nlstate ; jk++){    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
             for(m=-1, pos=0; m <=0 ; m++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
             pos += freq[jk][m][i];  #endif
         }    for (j=1;j<=n;j++) { 
              xi[j] *= xmin; 
          for(jk=1; jk <=nlstate ; jk++){      p[j] += xi[j]; 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    } 
              pp[jk] += freq[jk][m][i];    free_vector(xicom,1,n); 
          }    free_vector(pcom,1,n); 
            } 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
   
          for(jk=1; jk <=nlstate ; jk++){            /*************** powell ************************/
            if( i <= (int) agemax){  /*
              if(pos>=1.e-5){  Minimization of a function func of n variables. Input consists of an initial starting point
                probs[i][jk][j1]= pp[jk]/pos;  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
              }  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
            }  such that failure to decrease by more than this amount on one iteration signals doneness. On
          }  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
            function value at p , and iter is the number of iterations taken. The routine linmin is used.
         }   */
     }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   }              double (*func)(double [])) 
    { 
      void linmin(double p[], double xi[], int n, double *fret, 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);                double (*func)(double [])); 
   free_vector(pp,1,nlstate);    int i,ibig,j; 
      double del,t,*pt,*ptt,*xit;
 }  /* End of Freq */    double fp,fptt;
     double *xits;
 /************* Waves Concatenation ***************/    int niterf, itmp;
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    pt=vector(1,n); 
 {    ptt=vector(1,n); 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    xit=vector(1,n); 
      Death is a valid wave (if date is known).    xits=vector(1,n); 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    *fret=(*func)(p); 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    for (j=1;j<=n;j++) pt[j]=p[j]; 
      and mw[mi+1][i]. dh depends on stepm.      rcurr_time = time(NULL);  
      */    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
   int i, mi, m;      ibig=0; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      del=0.0; 
      double sum=0., jmean=0.;*/      rlast_time=rcurr_time;
       /* (void) gettimeofday(&curr_time,&tzp); */
   int j, k=0,jk, ju, jl;      rcurr_time = time(NULL);  
   double sum=0.;      curr_time = *localtime(&rcurr_time);
   jmin=1e+5;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
   jmax=-1;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   jmean=0.;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
   for(i=1; i<=imx; i++){     for (i=1;i<=n;i++) {
     mi=0;        printf(" %d %.12f",i, p[i]);
     m=firstpass;        fprintf(ficlog," %d %.12lf",i, p[i]);
     while(s[m][i] <= nlstate){        fprintf(ficrespow," %.12lf", p[i]);
       if(s[m][i]>=1)      }
         mw[++mi][i]=m;      printf("\n");
       if(m >=lastpass)      fprintf(ficlog,"\n");
         break;      fprintf(ficrespow,"\n");fflush(ficrespow);
       else      if(*iter <=3){
         m++;        tml = *localtime(&rcurr_time);
     }/* end while */        strcpy(strcurr,asctime(&tml));
     if (s[m][i] > nlstate){        rforecast_time=rcurr_time; 
       mi++;     /* Death is another wave */        itmp = strlen(strcurr);
       /* if(mi==0)  never been interviewed correctly before death */        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
          /* Only death is a correct wave */          strcurr[itmp-1]='\0';
       mw[mi][i]=m;        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
     }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         for(niterf=10;niterf<=30;niterf+=10){
     wav[i]=mi;          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
     if(mi==0)          forecast_time = *localtime(&rforecast_time);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          strcpy(strfor,asctime(&forecast_time));
   }          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   for(i=1; i<=imx; i++){          strfor[itmp-1]='\0';
     for(mi=1; mi<wav[i];mi++){          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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       if (stepm <=0)          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         dh[mi][i]=1;        }
       else{      }
         if (s[mw[mi+1][i]][i] > nlstate) {      for (i=1;i<=n;i++) { 
           if (agedc[i] < 2*AGESUP) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        fptt=(*fret); 
           if(j==0) j=1;  /* Survives at least one month after exam */  #ifdef DEBUG
           k=k+1;            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           if (j >= jmax) jmax=j;            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           if (j <= jmin) jmin=j;  #endif
           sum=sum+j;        printf("%d",i);fflush(stdout);
           /* if (j<10) printf("j=%d num=%d ",j,i); */        fprintf(ficlog,"%d",i);fflush(ficlog);
           }        linmin(p,xit,n,fret,func); 
         }        if (fabs(fptt-(*fret)) > del) { 
         else{          del=fabs(fptt-(*fret)); 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          ibig=i; 
           k=k+1;        } 
           if (j >= jmax) jmax=j;  #ifdef DEBUG
           else if (j <= jmin)jmin=j;        printf("%d %.12e",i,(*fret));
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        fprintf(ficlog,"%d %.12e",i,(*fret));
           sum=sum+j;        for (j=1;j<=n;j++) {
         }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         jk= j/stepm;          printf(" x(%d)=%.12e",j,xit[j]);
         jl= j -jk*stepm;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         ju= j -(jk+1)*stepm;        }
         if(jl <= -ju)        for(j=1;j<=n;j++) {
           dh[mi][i]=jk;          printf(" p(%d)=%.12e",j,p[j]);
         else          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
           dh[mi][i]=jk+1;        }
         if(dh[mi][i]==0)        printf("\n");
           dh[mi][i]=1; /* At least one step */        fprintf(ficlog,"\n");
       }  #endif
     }      } /* end i */
   }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   jmean=sum/k;  #ifdef DEBUG
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        int k[2],l;
  }        k[0]=1;
 /*********** Tricode ****************************/        k[1]=-1;
 void tricode(int *Tvar, int **nbcode, int imx)        printf("Max: %.12e",(*func)(p));
 {        fprintf(ficlog,"Max: %.12e",(*func)(p));
   int Ndum[20],ij=1, k, j, i;        for (j=1;j<=n;j++) {
   int cptcode=0;          printf(" %.12e",p[j]);
   cptcoveff=0;          fprintf(ficlog," %.12e",p[j]);
          }
   for (k=0; k<19; k++) Ndum[k]=0;        printf("\n");
   for (k=1; k<=7; k++) ncodemax[k]=0;        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for (j=1;j<=n;j++) {
     for (i=1; i<=imx; i++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       ij=(int)(covar[Tvar[j]][i]);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       Ndum[ij]++;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          }
       if (ij > cptcode) cptcode=ij;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
     for (i=0; i<=cptcode; i++) {  #endif
       if(Ndum[i]!=0) ncodemax[j]++;  
     }  
     ij=1;        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
     for (i=1; i<=ncodemax[j]; i++) {        free_vector(pt,1,n); 
       for (k=0; k<=19; k++) {        return; 
         if (Ndum[k] != 0) {      } 
           nbcode[Tvar[j]][ij]=k;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
           ij++;      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
         }        ptt[j]=2.0*p[j]-pt[j]; 
         if (ij > ncodemax[j]) break;        xit[j]=p[j]-pt[j]; 
       }          pt[j]=p[j]; 
     }      } 
   }        fptt=(*func)(ptt); 
       if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
  for (k=0; k<19; k++) Ndum[k]=0;        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
         /* From x1 (P0) distance of x2 is at h and x3 is 2h */
  for (i=1; i<=ncovmodel-2; i++) {        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       ij=Tvar[i];        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
       Ndum[ij]++;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
     }        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
         /* Thus we compare delta(2h) with observed f1-f3 */
  ij=1;        /* or best gain on one ancient line 'del' with total  */
  for (i=1; i<=10; i++) {        /* gain f1-f2 = f1 - f2 - 'del' with del  */
    if((Ndum[i]!=0) && (i<=ncov)){        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
      Tvaraff[ij]=i;  
      ij++;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
    }        t= t- del*SQR(fp-fptt);
  }        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
          fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
     cptcoveff=ij-1;  #ifdef DEBUG
 }        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
 /*********** Health Expectancies ****************/        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
 {        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   /* Health expectancies */  #endif
   int i, j, nhstepm, hstepm, h;        if (t < 0.0) { /* Then we use it for last direction */
   double age, agelim,hf;          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
   double ***p3mat;          for (j=1;j<=n;j++) { 
              xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
   fprintf(ficreseij,"# Health expectancies\n");            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   fprintf(ficreseij,"# Age");          }
   for(i=1; i<=nlstate;i++)          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     for(j=1; j<=nlstate;j++)          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
       fprintf(ficreseij," %1d-%1d",i,j);  
   fprintf(ficreseij,"\n");  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   hstepm=1*YEARM; /*  Every j years of age (in month) */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
   agelim=AGESUP;            fprintf(ficlog," %.12e",xit[j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     /* nhstepm age range expressed in number of stepm */          printf("\n");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          fprintf(ficlog,"\n");
     /* Typically if 20 years = 20*12/6=40 stepm */  #endif
     if (stepm >= YEARM) hstepm=1;        } /* end of t negative */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      } /* end if (fptt < fp)  */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  } 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    /**** Prevalence limit (stable or period prevalence)  ****************/
   
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(i=1; i<=nlstate;i++)  {
       for(j=1; j<=nlstate;j++)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){       matrix by transitions matrix until convergence is reached */
           eij[i][j][(int)age] +=p3mat[i][j][h];    
         }    int i, ii,j,k;
        double min, max, maxmin, maxmax,sumnew=0.;
     hf=1;    /* double **matprod2(); */ /* test */
     if (stepm >= YEARM) hf=stepm/YEARM;    double **out, cov[NCOVMAX+1], **pmij();
     fprintf(ficreseij,"%.0f",age );    double **newm;
     for(i=1; i<=nlstate;i++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       for(j=1; j<=nlstate;j++){    
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    for (ii=1;ii<=nlstate+ndeath;ii++)
       }      for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficreseij,"\n");        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
   }    
 }    cov[1]=1.;
     
 /************ Variance ******************/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 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)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 {      newm=savm;
   /* Variance of health expectancies */      /* Covariates have to be included here again */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      cov[2]=agefin;
   double **newm;      
   double **dnewm,**doldm;      for (k=1; k<=cptcovn;k++) {
   int i, j, nhstepm, hstepm, h;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int k, cptcode;        /*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]]);*/
   double *xp;      }
   double **gp, **gm;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   double ***gradg, ***trgradg;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   double ***p3mat;      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   double age,agelim;      
   int theta;      /*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]);*/
    fprintf(ficresvij,"# Covariances of life expectancies\n");      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   fprintf(ficresvij,"# Age");      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   for(i=1; i<=nlstate;i++)      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
     for(j=1; j<=nlstate;j++)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      
   fprintf(ficresvij,"\n");      savm=oldm;
       oldm=newm;
   xp=vector(1,npar);      maxmax=0.;
   dnewm=matrix(1,nlstate,1,npar);      for(j=1;j<=nlstate;j++){
   doldm=matrix(1,nlstate,1,nlstate);        min=1.;
          max=0.;
   hstepm=1*YEARM; /* Every year of age */        for(i=1; i<=nlstate; i++) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          sumnew=0;
   agelim = AGESUP;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          prlim[i][j]= newm[i][j]/(1-sumnew);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
     if (stepm >= YEARM) hstepm=1;          max=FMAX(max,prlim[i][j]);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          min=FMIN(min,prlim[i][j]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        maxmin=max-min;
     gp=matrix(0,nhstepm,1,nlstate);        maxmax=FMAX(maxmax,maxmin);
     gm=matrix(0,nhstepm,1,nlstate);      } /* j loop */
       if(maxmax < ftolpl){
     for(theta=1; theta <=npar; theta++){        return prlim;
       for(i=1; i<=npar; i++){ /* Computes gradient */      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    } /* age loop */
       }    return prlim; /* should not reach here */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
   /*************** transition probabilities ***************/ 
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
           prlim[i][i]=probs[(int)age][i][ij];  {
       }    /* 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
       for(j=1; j<= nlstate; j++){       model to the ncovmodel covariates (including constant and age).
         for(h=0; h<=nhstepm; h++){       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];       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,
       for(i=1; i<=npar; i++) /* Computes gradient */       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       Outputs ps[i][j] the probability to be observed in j being in j according to
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    */
      double s1, lnpijopii;
       if (popbased==1) {    /*double t34;*/
         for(i=1; i<=nlstate;i++)    int i,j, nc, ii, jj;
           prlim[i][i]=probs[(int)age][i][ij];  
       }      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
       for(j=1; j<= nlstate; j++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         for(h=0; h<=nhstepm; h++){            /*lnpijopii += param[i][j][nc]*cov[nc];*/
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }          }
       }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       for(j=1; j<= nlstate; j++)        }
         for(h=0; h<=nhstepm; h++){        for(j=i+1; j<=nlstate+ndeath;j++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         }            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     } /* End theta */            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     for(h=0; h<=nhstepm; h++)        }
       for(j=1; j<=nlstate;j++)      }
         for(theta=1; theta <=npar; theta++)      
           trgradg[h][j][theta]=gradg[h][theta][j];      for(i=1; i<= nlstate; i++){
         s1=0;
     for(i=1;i<=nlstate;i++)        for(j=1; j<i; j++){
       for(j=1;j<=nlstate;j++)          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         vareij[i][j][(int)age] =0.;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     for(h=0;h<=nhstepm;h++){        }
       for(k=0;k<=nhstepm;k++){        for(j=i+1; j<=nlstate+ndeath; j++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         for(i=1;i<=nlstate;i++)        }
           for(j=1;j<=nlstate;j++)        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
             vareij[i][j][(int)age] += doldm[i][j];        ps[i][i]=1./(s1+1.);
       }        /* Computing other pijs */
     }        for(j=1; j<i; j++)
     h=1;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     if (stepm >= YEARM) h=stepm/YEARM;        for(j=i+1; j<=nlstate+ndeath; j++)
     fprintf(ficresvij,"%.0f ",age );          ps[i][j]= exp(ps[i][j])*ps[i][i];
     for(i=1; i<=nlstate;i++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for(j=1; j<=nlstate;j++){      } /* end i */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      
       }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     fprintf(ficresvij,"\n");        for(jj=1; jj<= nlstate+ndeath; jj++){
     free_matrix(gp,0,nhstepm,1,nlstate);          ps[ii][jj]=0;
     free_matrix(gm,0,nhstepm,1,nlstate);          ps[ii][ii]=1;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
   } /* End age */      
        /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   free_vector(xp,1,npar);      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   free_matrix(doldm,1,nlstate,1,npar);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   free_matrix(dnewm,1,nlstate,1,nlstate);      /*   } */
       /*   printf("\n "); */
 }      /* } */
       /* printf("\n ");printf("%lf ",cov[2]);*/
 /************ Variance of prevlim ******************/      /*
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
 {        goto end;*/
   /* Variance of prevalence limit */      return ps;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  }
   double **newm;  
   double **dnewm,**doldm;  /**************** Product of 2 matrices ******************/
   int i, j, nhstepm, hstepm;  
   int k, cptcode;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   double *xp;  {
   double *gp, *gm;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double **gradg, **trgradg;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double age,agelim;    /* in, b, out are matrice of pointers which should have been initialized 
   int theta;       before: only the contents of out is modified. The function returns
           a pointer to pointers identical to out */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    int i, j, k;
   fprintf(ficresvpl,"# Age");    for(i=nrl; i<= nrh; i++)
   for(i=1; i<=nlstate;i++)      for(k=ncolol; k<=ncoloh; k++){
       fprintf(ficresvpl," %1d-%1d",i,i);        out[i][k]=0.;
   fprintf(ficresvpl,"\n");        for(j=ncl; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
   xp=vector(1,npar);      }
   dnewm=matrix(1,nlstate,1,npar);    return out;
   doldm=matrix(1,nlstate,1,nlstate);  }
    
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  /************* Higher Matrix Product ***************/
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  {
     if (stepm >= YEARM) hstepm=1;    /* Computes the transition matrix starting at age 'age' over 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       'nhstepm*hstepm*stepm' months (i.e. until
     gradg=matrix(1,npar,1,nlstate);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     gp=vector(1,nlstate);       nhstepm*hstepm matrices. 
     gm=vector(1,nlstate);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
     for(theta=1; theta <=npar; theta++){       for the memory).
       for(i=1; i<=npar; i++){ /* Computes gradient */       Model is determined by parameters x and covariates have to be 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       included manually here. 
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       */
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];    int i, j, d, h, k;
        double **out, cov[NCOVMAX+1];
       for(i=1; i<=npar; i++) /* Computes gradient */    double **newm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* Hstepm could be zero and should return the unit matrix */
       for(i=1;i<=nlstate;i++)    for (i=1;i<=nlstate+ndeath;i++)
         gm[i] = prlim[i][i];      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
       for(i=1;i<=nlstate;i++)        po[i][j][0]=(i==j ? 1.0 : 0.0);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      }
     } /* End theta */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
     trgradg =matrix(1,nlstate,1,npar);      for(d=1; d <=hstepm; d++){
         newm=savm;
     for(j=1; j<=nlstate;j++)        /* Covariates have to be included here again */
       for(theta=1; theta <=npar; theta++)        cov[1]=1.;
         trgradg[j][theta]=gradg[theta][j];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) 
     for(i=1;i<=nlstate;i++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       varpl[i][(int)age] =0.;        for (k=1; k<=cptcovage;k++)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
     for(i=1;i<=nlstate;i++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
   
     fprintf(ficresvpl,"%.0f ",age );        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for(i=1; i<=nlstate;i++)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     fprintf(ficresvpl,"\n");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_vector(gp,1,nlstate);        savm=oldm;
     free_vector(gm,1,nlstate);        oldm=newm;
     free_matrix(gradg,1,npar,1,nlstate);      }
     free_matrix(trgradg,1,nlstate,1,npar);      for(i=1; i<=nlstate+ndeath; i++)
   } /* End age */        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
   free_vector(xp,1,npar);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   free_matrix(doldm,1,nlstate,1,npar);        }
   free_matrix(dnewm,1,nlstate,1,nlstate);      /*printf("h=%d ",h);*/
     } /* end h */
 }  /*     printf("\n H=%d \n",h); */
     return po;
 /************ Variance of one-step probabilities  ******************/  }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  
 {  #ifdef NLOPT
   int i, j;    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   int k=0, cptcode;    double fret;
   double **dnewm,**doldm;    double *xt;
   double *xp;    int j;
   double *gp, *gm;    myfunc_data *d2 = (myfunc_data *) pd;
   double **gradg, **trgradg;  /* xt = (p1-1); */
   double age,agelim, cov[NCOVMAX];    xt=vector(1,n); 
   int theta;    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   char fileresprob[FILENAMELENGTH];  
     fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
   strcpy(fileresprob,"prob");    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
   strcat(fileresprob,fileres);    printf("Function = %.12lf ",fret);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf("Problem with resultfile: %s\n", fileresprob);    printf("\n");
   }   free_vector(xt,1,n);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    return fret;
    }
   #endif
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  /*************** log-likelihood *************/
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  double func( double *x)
    {
   cov[1]=1;    int i, ii, j, k, mi, d, kk;
   for (age=bage; age<=fage; age ++){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     cov[2]=age;    double **out;
     gradg=matrix(1,npar,1,9);    double sw; /* Sum of weights */
     trgradg=matrix(1,9,1,npar);    double lli; /* Individual log likelihood */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    int s1, s2;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    double bbh, survp;
        long ipmx;
     for(theta=1; theta <=npar; theta++){    /*extern weight */
       for(i=1; i<=npar; i++)    /* We are differentiating ll according to initial status */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
          /*for(i=1;i<imx;i++) 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      printf(" %d\n",s[4][i]);
        */
       k=0;  
       for(i=1; i<= (nlstate+ndeath); i++){    ++countcallfunc;
         for(j=1; j<=(nlstate+ndeath);j++){  
            k=k+1;    cov[1]=1.;
           gp[k]=pmmij[i][j];  
         }    for(k=1; k<=nlstate; k++) ll[k]=0.;
       }  
     if(mle==1){
       for(i=1; i<=npar; i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        /* Computes the values of the ncovmodel covariates of the model
               depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
            Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
       pmij(pmmij,cov,ncovmodel,xp,nlstate);           to be observed in j being in i according to the model.
       k=0;         */
       for(i=1; i<=(nlstate+ndeath); i++){        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
         for(j=1; j<=(nlstate+ndeath);j++){          cov[2+k]=covar[Tvar[k]][i];
           k=k+1;        }
           gm[k]=pmmij[i][j];        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
         }           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       }           has been calculated etc */
              for(mi=1; mi<= wav[i]-1; mi++){
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            }
       for(theta=1; theta <=npar; theta++)          for(d=0; d<dh[mi][i]; d++){
       trgradg[j][theta]=gradg[theta][j];            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            for (kk=1; kk<=cptcovage;kk++) {
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
             }
      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));
      k=0;            savm=oldm;
      for(i=1; i<=(nlstate+ndeath); i++){            oldm=newm;
        for(j=1; j<=(nlstate+ndeath);j++){          } /* end mult */
          k=k+1;        
          gm[k]=pmmij[i][j];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         }          /* But now since version 0.9 we anticipate for bias at large stepm.
      }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
                 * (in months) between two waves is not a multiple of stepm, we rounded to 
      /*printf("\n%d ",(int)age);           * the nearest (and in case of equal distance, to the lowest) interval but now
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
      }*/           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
   fprintf(ficresprob,"\n%d ",(int)age);           * For stepm > 1 the results are less biased than in previous versions. 
            */
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          s1=s[mw[mi][i]][i];
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          s2=s[mw[mi+1][i]][i];
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          bbh=(double)bh[mi][i]/(double)stepm; 
   }          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));           */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          if( s2 > nlstate){ 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            /* 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 
  free_vector(xp,1,npar);               die between last step unit time and current  step unit time, 
 fclose(ficresprob);               which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
 }               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
 /******************* Printing html file ***********/          health state: the date of the interview describes the actual state
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){          and not the date of a change in health state. The former idea was
   int jj1, k1, i1, cpt;          to consider that at each interview the state was recorded
   FILE *fichtm;          (healthy, disable or death) and IMaCh was corrected; but when we
   /*char optionfilehtm[FILENAMELENGTH];*/          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
   strcpy(optionfilehtm,optionfile);          contribution is smaller and very dependent of the step unit
   strcat(optionfilehtm,".htm");          stepm. It is no more the probability to die between last interview
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          and month of death but the probability to survive from last
     printf("Problem with %s \n",optionfilehtm), exit(0);          interview up to one month before death multiplied by the
   }          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">          mortality artificially. The bad side is that we add another loop
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          which slows down the processing. The difference can be up to 10%
           lower mortality.
 Total number of observations=%d <br>            */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>            lli=log(out[s1][s2] - savm[s1][s2]);
 <hr  size=\"2\" color=\"#EC5E5E\">  
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          } else if  (s2==-2) {
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>            for (j=1,survp=0. ; j<=nlstate; j++) 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            /*survp += out[s1][j]; */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>            lli= log(survp);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          else if  (s2==-4) { 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>            for (j=3,survp=0. ; j<=nlstate; j++)  
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);            lli= log(survp); 
            } 
 fprintf(fichtm," <li>Graphs</li><p>");  
           else if  (s2==-5) { 
  m=cptcoveff;            for (j=1,survp=0. ; j<=2; j++)  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
  jj1=0;          } 
  for(k1=1; k1<=m;k1++){          
    for(i1=1; i1<=ncodemax[k1];i1++){          else{
        jj1++;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        if (cptcovn > 0) {            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          } 
          for (cpt=1; cpt<=cptcoveff;cpt++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          /*if(lli ==000.0)*/
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          /*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); */
        }          ipmx +=1;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          sw += weight[i];
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        for(cpt=1; cpt<nlstate;cpt++){        } /* end of wave */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      } /* end of individual */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    }  else if(mle==2){
        }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(cpt=1; cpt<=nlstate;cpt++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        for(mi=1; mi<= wav[i]-1; mi++){
 interval) in state (%d): v%s%d%d.gif <br>          for (ii=1;ii<=nlstate+ndeath;ii++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              for (j=1;j<=nlstate+ndeath;j++){
      }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      for(cpt=1; cpt<=nlstate;cpt++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            }
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(d=0; d<=dh[mi][i]; d++){
      }            newm=savm;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 health expectancies in states (1) and (2): e%s%d.gif<br>            for (kk=1; kk<=cptcovage;kk++) {
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 fprintf(fichtm,"\n</body>");            }
    }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 fclose(fichtm);            savm=oldm;
 }            oldm=newm;
           } /* end mult */
 /******************* Gnuplot file **************/        
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          bbh=(double)bh[mi][i]/(double)stepm; 
           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 */
   strcpy(optionfilegnuplot,optionfilefiname);          ipmx +=1;
   strcat(optionfilegnuplot,".plt");          sw += weight[i];
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     printf("Problem with file %s",optionfilegnuplot);        } /* end of wave */
   }      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
 #ifdef windows      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficgp,"cd \"%s\" \n",pathc);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 #endif        for(mi=1; mi<= wav[i]-1; mi++){
 m=pow(2,cptcoveff);          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
  /* 1eme*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (cpt=1; cpt<= nlstate ; cpt ++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    for (k1=1; k1<= m ; k1 ++) {            }
           for(d=0; d<dh[mi][i]; d++){
 #ifdef windows            newm=savm;
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 #endif            for (kk=1; kk<=cptcovage;kk++) {
 #ifdef unix              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);            }
 #endif            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 for (i=1; i<= nlstate ; i ++) {            savm=oldm;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            oldm=newm;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          } /* end mult */
 }        
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          s1=s[mw[mi][i]][i];
     for (i=1; i<= nlstate ; i ++) {          s2=s[mw[mi+1][i]][i];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          bbh=(double)bh[mi][i]/(double)stepm; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 }          ipmx +=1;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          sw += weight[i];
      for (i=1; i<= nlstate ; i ++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        } /* end of wave */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      } /* end of individual */
 }      }else if (mle==4){  /* ml=4 no inter-extrapolation */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 #ifdef unix        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 fprintf(ficgp,"\nset ter gif small size 400,300");        for(mi=1; mi<= wav[i]-1; mi++){
 #endif          for (ii=1;ii<=nlstate+ndeath;ii++)
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            for (j=1;j<=nlstate+ndeath;j++){
    }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*2 eme*/            }
           for(d=0; d<dh[mi][i]; d++){
   for (k1=1; k1<= m ; k1 ++) {            newm=savm;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
     for (i=1; i<= nlstate+1 ; i ++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       k=2*i;            }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          
       for (j=1; j<= nlstate+1 ; j ++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   else fprintf(ficgp," \%%*lf (\%%*lf)");            savm=oldm;
 }              oldm=newm;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          } /* end mult */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          s1=s[mw[mi][i]][i];
       for (j=1; j<= nlstate+1 ; j ++) {          s2=s[mw[mi+1][i]][i];
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if( s2 > nlstate){ 
         else fprintf(ficgp," \%%*lf (\%%*lf)");            lli=log(out[s1][s2] - savm[s1][s2]);
 }            }else{
       fprintf(ficgp,"\" t\"\" w l 0,");            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {          ipmx +=1;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          sw += weight[i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 }    /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        } /* end of wave */
       else fprintf(ficgp,"\" t\"\" w l 0,");      } /* end of individual */
     }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      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++){
   /*3eme*/          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   for (k1=1; k1<= m ; k1 ++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (cpt=1; cpt<= nlstate ; cpt ++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       k=2+nlstate*(cpt-1);            }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          for(d=0; d<dh[mi][i]; d++){
       for (i=1; i< nlstate ; i ++) {            newm=savm;
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
     }          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* CV preval stat */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (k1=1; k1<= m ; k1 ++) {            savm=oldm;
     for (cpt=1; cpt<nlstate ; cpt ++) {            oldm=newm;
       k=3;          } /* end mult */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);        
           s1=s[mw[mi][i]][i];
       for (i=1; i< nlstate ; i ++)          s2=s[mw[mi+1][i]][i];
         fprintf(ficgp,"+$%d",k+i+1);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          ipmx +=1;
                sw += weight[i];
       l=3+(nlstate+ndeath)*cpt;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       for (i=1; i< nlstate ; i ++) {        } /* end of wave */
         l=3+(nlstate+ndeath)*cpt;      } /* end of individual */
         fprintf(ficgp,"+$%d",l+i+1);    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    return -l;
   }    }
    
   /* proba elementaires */  /*************** log-likelihood *************/
    for(i=1,jk=1; i <=nlstate; i++){  double funcone( double *x)
     for(k=1; k <=(nlstate+ndeath); k++){  {
       if (k != i) {    /* Same as likeli but slower because of a lot of printf and if */
         for(j=1; j <=ncovmodel; j++){    int i, ii, j, k, mi, d, kk;
            double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    double **out;
           jk++;    double lli; /* Individual log likelihood */
           fprintf(ficgp,"\n");    double llt;
         }    int s1, s2;
       }    double bbh, survp;
     }    /*extern weight */
     }    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(jk=1; jk <=m; jk++) {    /*for(i=1;i<imx;i++) 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      printf(" %d\n",s[4][i]);
    i=1;    */
    for(k2=1; k2<=nlstate; k2++) {    cov[1]=1.;
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
        if (k != k2){  
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 ij=1;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(j=3; j <=ncovmodel; j++) {      for(mi=1; mi<= wav[i]-1; mi++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for (ii=1;ii<=nlstate+ndeath;ii++)
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          for (j=1;j<=nlstate+ndeath;j++){
             ij++;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           else          }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for(d=0; d<dh[mi][i]; d++){
         }          newm=savm;
           fprintf(ficgp,")/(1");          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                  for (kk=1; kk<=cptcovage;kk++) {
         for(k1=1; k1 <=nlstate; k1++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          }
 ij=1;          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           for(j=3; j <=ncovmodel; j++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
             ij++;          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           }          savm=oldm;
           else          oldm=newm;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        } /* end mult */
           }        
           fprintf(ficgp,")");        s1=s[mw[mi][i]][i];
         }        s2=s[mw[mi+1][i]][i];
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        bbh=(double)bh[mi][i]/(double)stepm; 
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        /* bias is positive if real duration
         i=i+ncovmodel;         * is higher than the multiple of stepm and negative otherwise.
        }         */
      }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
    }          lli=log(out[s1][s2] - savm[s1][s2]);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        } else if  (s2==-2) {
    }          for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   fclose(ficgp);          lli= log(survp);
 }  /* end gnuplot */        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
 /*************** Moving average **************/          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 */
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){        } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   int i, cpt, cptcod;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     for (agedeb=agemin; agedeb<=fage; agedeb++)          lli=log(out[s1][s2]); /* Original formula */
       for (i=1; i<=nlstate;i++)        } else{  /* mle=0 back to 1 */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           mobaverage[(int)agedeb][i][cptcod]=0.;          /*lli=log(out[s1][s2]); */ /* Original formula */
            } /* End of if */
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){        ipmx +=1;
       for (i=1; i<=nlstate;i++){        sw += weight[i];
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for (cpt=0;cpt<=4;cpt++){        /*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]); */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        if(globpr){
           }          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;   %11.6f %11.6f %11.6f ", \
         }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                llt +=ll[k]*gipmx/gsw;
 }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
 /***********************************************/          fprintf(ficresilk," %10.6f\n", -llt);
 /**************** Main Program *****************/        }
 /***********************************************/      } /* end of wave */
     } /* end of individual */
 int main(int argc, char *argv[])    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 {    /* 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 */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    if(globpr==0){ /* First time we count the contributions and weights */
   double agedeb, agefin,hf;      gipmx=ipmx;
   double agemin=1.e20, agemax=-1.e20;      gsw=sw;
     }
   double fret;    return -l;
   double **xi,tmp,delta;  }
   
   double dum; /* Dummy variable */  
   double ***p3mat;  /*************** function likelione ***********/
   int *indx;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   char line[MAXLINE], linepar[MAXLINE];  {
   char title[MAXLINE];    /* This routine should help understanding what is done with 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];       the selection of individuals/waves and
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];       to check the exact contribution to the likelihood.
         Plotting could be done.
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];     */
     int k;
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];    if(*globpri !=0){ /* Just counts and sums, no printings */
   char popfile[FILENAMELENGTH];      strcpy(fileresilk,"ilk"); 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      strcat(fileresilk,fileres);
   int firstobs=1, lastobs=10;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   int sdeb, sfin; /* Status at beginning and end */        printf("Problem with resultfile: %s\n", fileresilk);
   int c,  h , cpt,l;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   int ju,jl, mi;      }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      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");
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   int mobilav=0,popforecast=0;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   int hstepm, nhstepm;      for(k=1; k<=nlstate; k++) 
   int *popage;/*boolprev=0 if date and zero if wave*/        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;    *fretone=(*funcone)(p);
   double **prlim;    if(*globpri !=0){
   double *severity;      fclose(ficresilk);
   double ***param; /* Matrix of parameters */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   double  *p;      fflush(fichtm); 
   double **matcov; /* Matrix of covariance */    } 
   double ***delti3; /* Scale */    return;
   double *delti; /* Scale */  }
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;  /*********** Maximum Likelihood Estimation ***************/
   double kk1, kk2;  
   double *popeffectif,*popcount;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;  {
   double yp,yp1,yp2;    int i,j, iter=0;
     double **xi;
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";    double fret;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   
   char z[1]="c", occ;  #ifdef NLOPT
 #include <sys/time.h>    int creturn;
 #include <time.h>    nlopt_opt opt;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
      double *lb;
   /* long total_usecs;    double minf; /* the minimum objective value, upon return */
   struct timeval start_time, end_time;    double * p1; /* Shifted parameters from 0 instead of 1 */
      myfunc_data dinst, *d = &dinst;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  #endif
   
   
   printf("\n%s",version);    xi=matrix(1,npar,1,npar);
   if(argc <=1){    for (i=1;i<=npar;i++)
     printf("\nEnter the parameter file name: ");      for (j=1;j<=npar;j++)
     scanf("%s",pathtot);        xi[i][j]=(i==j ? 1.0 : 0.0);
   }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   else{    strcpy(filerespow,"pow"); 
     strcpy(pathtot,argv[1]);    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      printf("Problem with resultfile: %s\n", filerespow);
   /*cygwin_split_path(pathtot,path,optionfile);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    }
   /* cutv(path,optionfile,pathtot,'\\');*/    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      for(j=1;j<=nlstate+ndeath;j++)
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   chdir(path);    fprintf(ficrespow,"\n");
   replace(pathc,path);  #ifdef POWELL
     powell(p,xi,npar,ftol,&iter,&fret,func);
 /*-------- arguments in the command line --------*/  #endif
   
   strcpy(fileres,"r");  #ifdef NLOPT
   strcat(fileres, optionfilefiname);  #ifdef NEWUOA
   strcat(fileres,".txt");    /* Other files have txt extension */    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
   /*---------arguments file --------*/    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    lb=vector(0,npar-1);
     printf("Problem with optionfile %s\n",optionfile);    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     goto end;    nlopt_set_lower_bounds(opt, lb);
   }    nlopt_set_initial_step1(opt, 0.1);
     
   strcpy(filereso,"o");    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   strcat(filereso,fileres);    d->function = func;
   if((ficparo=fopen(filereso,"w"))==NULL) {    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    nlopt_set_min_objective(opt, myfunc, d);
   }    nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
   /* Reads comments: lines beginning with '#' */      printf("nlopt failed! %d\n",creturn); 
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    else {
     fgets(line, MAXLINE, ficpar);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
     puts(line);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
     fputs(line,ficparo);      iter=1; /* not equal */
   }    }
   ungetc(c,ficpar);    nlopt_destroy(opt);
   #endif
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    free_matrix(xi,1,npar,1,npar);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    fclose(ficrespow);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
 while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     ungetc(c,ficpar);    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fgets(line, MAXLINE, ficpar);  
     puts(line);  }
     fputs(line,ficparo);  
   }  /**** Computes Hessian and covariance matrix ***/
   ungetc(c,ficpar);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    {
        double  **a,**y,*x,pd;
   covar=matrix(0,NCOVMAX,1,n);    double **hess;
   cptcovn=0;    int i, j;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    int *indx;
   
   ncovmodel=2+cptcovn;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      void lubksb(double **a, int npar, int *indx, double b[]) ;
   /* Read guess parameters */    void ludcmp(double **a, int npar, int *indx, double *d) ;
   /* Reads comments: lines beginning with '#' */    double gompertz(double p[]);
   while((c=getc(ficpar))=='#' && c!= EOF){    hess=matrix(1,npar,1,npar);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    printf("\nCalculation of the hessian matrix. Wait...\n");
     puts(line);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     fputs(line,ficparo);    for (i=1;i<=npar;i++){
   }      printf("%d",i);fflush(stdout);
   ungetc(c,ficpar);      fprintf(ficlog,"%d",i);fflush(ficlog);
       
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     for(i=1; i <=nlstate; i++)      
     for(j=1; j <=nlstate+ndeath-1; j++){      /*  printf(" %f ",p[i]);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       fprintf(ficparo,"%1d%1d",i1,j1);    }
       printf("%1d%1d",i,j);    
       for(k=1; k<=ncovmodel;k++){    for (i=1;i<=npar;i++) {
         fscanf(ficpar," %lf",&param[i][j][k]);      for (j=1;j<=npar;j++)  {
         printf(" %lf",param[i][j][k]);        if (j>i) { 
         fprintf(ficparo," %lf",param[i][j][k]);          printf(".%d%d",i,j);fflush(stdout);
       }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       fscanf(ficpar,"\n");          hess[i][j]=hessij(p,delti,i,j,func,npar);
       printf("\n");          
       fprintf(ficparo,"\n");          hess[j][i]=hess[i][j];    
     }          /*printf(" %lf ",hess[i][j]);*/
          }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      }
     }
   p=param[1][1];    printf("\n");
      fprintf(ficlog,"\n");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     ungetc(c,ficpar);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     fgets(line, MAXLINE, ficpar);    
     puts(line);    a=matrix(1,npar,1,npar);
     fputs(line,ficparo);    y=matrix(1,npar,1,npar);
   }    x=vector(1,npar);
   ungetc(c,ficpar);    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    ludcmp(a,npar,indx,&pd);
   for(i=1; i <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){    for (j=1;j<=npar;j++) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for (i=1;i<=npar;i++) x[i]=0;
       printf("%1d%1d",i,j);      x[j]=1;
       fprintf(ficparo,"%1d%1d",i1,j1);      lubksb(a,npar,indx,x);
       for(k=1; k<=ncovmodel;k++){      for (i=1;i<=npar;i++){ 
         fscanf(ficpar,"%le",&delti3[i][j][k]);        matcov[i][j]=x[i];
         printf(" %le",delti3[i][j][k]);      }
         fprintf(ficparo," %le",delti3[i][j][k]);    }
       }  
       fscanf(ficpar,"\n");    printf("\n#Hessian matrix#\n");
       printf("\n");    fprintf(ficlog,"\n#Hessian matrix#\n");
       fprintf(ficparo,"\n");    for (i=1;i<=npar;i++) { 
     }      for (j=1;j<=npar;j++) { 
   }        printf("%.3e ",hess[i][j]);
   delti=delti3[1][1];        fprintf(ficlog,"%.3e ",hess[i][j]);
        }
   /* Reads comments: lines beginning with '#' */      printf("\n");
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"\n");
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);  
     puts(line);    /* Recompute Inverse */
     fputs(line,ficparo);    for (i=1;i<=npar;i++)
   }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   ungetc(c,ficpar);    ludcmp(a,npar,indx,&pd);
    
   matcov=matrix(1,npar,1,npar);    /*  printf("\n#Hessian matrix recomputed#\n");
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);    for (j=1;j<=npar;j++) {
     printf("%s",str);      for (i=1;i<=npar;i++) x[i]=0;
     fprintf(ficparo,"%s",str);      x[j]=1;
     for(j=1; j <=i; j++){      lubksb(a,npar,indx,x);
       fscanf(ficpar," %le",&matcov[i][j]);      for (i=1;i<=npar;i++){ 
       printf(" %.5le",matcov[i][j]);        y[i][j]=x[i];
       fprintf(ficparo," %.5le",matcov[i][j]);        printf("%.3e ",y[i][j]);
     }        fprintf(ficlog,"%.3e ",y[i][j]);
     fscanf(ficpar,"\n");      }
     printf("\n");      printf("\n");
     fprintf(ficparo,"\n");      fprintf(ficlog,"\n");
   }    }
   for(i=1; i <=npar; i++)    */
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];    free_matrix(a,1,npar,1,npar);
        free_matrix(y,1,npar,1,npar);
   printf("\n");    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
     /*-------- data file ----------*/  
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;  }
     }  
     fprintf(ficres,"#%s\n",version);  /*************** hessian matrix ****************/
      double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     if((fic=fopen(datafile,"r"))==NULL)    {  {
       printf("Problem with datafile: %s\n", datafile);goto end;    int i;
     }    int l=1, lmax=20;
     double k1,k2;
     n= lastobs;    double p2[MAXPARM+1]; /* identical to x */
     severity = vector(1,maxwav);    double res;
     outcome=imatrix(1,maxwav+1,1,n);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     num=ivector(1,n);    double fx;
     moisnais=vector(1,n);    int k=0,kmax=10;
     annais=vector(1,n);    double l1;
     moisdc=vector(1,n);  
     andc=vector(1,n);    fx=func(x);
     agedc=vector(1,n);    for (i=1;i<=npar;i++) p2[i]=x[i];
     cod=ivector(1,n);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
     weight=vector(1,n);      l1=pow(10,l);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      delts=delt;
     mint=matrix(1,maxwav,1,n);      for(k=1 ; k <kmax; k=k+1){
     anint=matrix(1,maxwav,1,n);        delt = delta*(l1*k);
     s=imatrix(1,maxwav+1,1,n);        p2[theta]=x[theta] +delt;
     adl=imatrix(1,maxwav+1,1,n);            k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
     tab=ivector(1,NCOVMAX);        p2[theta]=x[theta]-delt;
     ncodemax=ivector(1,8);        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
     i=1;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     while (fgets(line, MAXLINE, fic) != NULL)    {        
       if ((i >= firstobs) && (i <=lastobs)) {  #ifdef DEBUGHESS
                printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         for (j=maxwav;j>=1;j--){        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);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  #endif
           strcpy(line,stra);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          k=kmax;
         }        }
                else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          k=kmax; l=lmax*10;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          delts=delt;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        }
       }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    }
         for (j=ncov;j>=1;j--){    delti[theta]=delts;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    return res; 
         }    
         num[i]=atol(stra);  }
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  {
     int i;
         i=i+1;    int l=1, lmax=20;
       }    double k1,k2,k3,k4,res,fx;
     }    double p2[MAXPARM+1];
     /* printf("ii=%d", ij);    int k;
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */    fx=func(x);
     for (k=1; k<=2; k++) {
   /* for (i=1; i<=imx; i++){      for (i=1;i<=npar;i++) p2[i]=x[i];
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      p2[thetai]=x[thetai]+delti[thetai]/k;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      k1=func(p2)-fx;
     }    
       p2[thetai]=x[thetai]+delti[thetai]/k;
     for (i=1; i<=imx; i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/      k2=func(p2)-fx;
     
   /* Calculation of the number of parameter from char model*/      p2[thetai]=x[thetai]-delti[thetai]/k;
   Tvar=ivector(1,15);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   Tprod=ivector(1,15);      k3=func(p2)-fx;
   Tvaraff=ivector(1,15);    
   Tvard=imatrix(1,15,1,2);      p2[thetai]=x[thetai]-delti[thetai]/k;
   Tage=ivector(1,15);            p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          k4=func(p2)-fx;
   if (strlen(model) >1){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     j=0, j1=0, k1=1, k2=1;  #ifdef DEBUG
     j=nbocc(model,'+');      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);
     j1=nbocc(model,'*');      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);
     cptcovn=j+1;  #endif
     cptcovprod=j1;    }
        return res;
      }
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  /************** Inverse of matrix **************/
       printf("Error. Non available option model=%s ",model);  void ludcmp(double **a, int n, int *indx, double *d) 
       goto end;  { 
     }    int i,imax,j,k; 
        double big,dum,sum,temp; 
     for(i=(j+1); i>=1;i--){    double *vv; 
       cutv(stra,strb,modelsav,'+');   
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    vv=vector(1,n); 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    *d=1.0; 
       /*scanf("%d",i);*/    for (i=1;i<=n;i++) { 
       if (strchr(strb,'*')) {      big=0.0; 
         cutv(strd,strc,strb,'*');      for (j=1;j<=n;j++) 
         if (strcmp(strc,"age")==0) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
           cptcovprod--;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           cutv(strb,stre,strd,'V');      vv[i]=1.0/big; 
           Tvar[i]=atoi(stre);    } 
           cptcovage++;    for (j=1;j<=n;j++) { 
             Tage[cptcovage]=i;      for (i=1;i<j;i++) { 
             /*printf("stre=%s ", stre);*/        sum=a[i][j]; 
         }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         else if (strcmp(strd,"age")==0) {        a[i][j]=sum; 
           cptcovprod--;      } 
           cutv(strb,stre,strc,'V');      big=0.0; 
           Tvar[i]=atoi(stre);      for (i=j;i<=n;i++) { 
           cptcovage++;        sum=a[i][j]; 
           Tage[cptcovage]=i;        for (k=1;k<j;k++) 
         }          sum -= a[i][k]*a[k][j]; 
         else {        a[i][j]=sum; 
           cutv(strb,stre,strc,'V');        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           Tvar[i]=ncov+k1;          big=dum; 
           cutv(strb,strc,strd,'V');          imax=i; 
           Tprod[k1]=i;        } 
           Tvard[k1][1]=atoi(strc);      } 
           Tvard[k1][2]=atoi(stre);      if (j != imax) { 
           Tvar[cptcovn+k2]=Tvard[k1][1];        for (k=1;k<=n;k++) { 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          dum=a[imax][k]; 
           for (k=1; k<=lastobs;k++)          a[imax][k]=a[j][k]; 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          a[j][k]=dum; 
           k1++;        } 
           k2=k2+2;        *d = -(*d); 
         }        vv[imax]=vv[j]; 
       }      } 
       else {      indx[j]=imax; 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      if (a[j][j] == 0.0) a[j][j]=TINY; 
        /*  scanf("%d",i);*/      if (j != n) { 
       cutv(strd,strc,strb,'V');        dum=1.0/(a[j][j]); 
       Tvar[i]=atoi(strc);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       }      } 
       strcpy(modelsav,stra);      } 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    free_vector(vv,1,n);  /* Doesn't work */
         scanf("%d",i);*/  ;
     }  } 
 }  
    void lubksb(double **a, int n, int *indx, double b[]) 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  { 
   printf("cptcovprod=%d ", cptcovprod);    int i,ii=0,ip,j; 
   scanf("%d ",i);*/    double sum; 
     fclose(fic);   
     for (i=1;i<=n;i++) { 
     /*  if(mle==1){*/      ip=indx[i]; 
     if (weightopt != 1) { /* Maximisation without weights*/      sum=b[ip]; 
       for(i=1;i<=n;i++) weight[i]=1.0;      b[ip]=b[i]; 
     }      if (ii) 
     /*-calculation of age at interview from date of interview and age at death -*/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     agev=matrix(1,maxwav,1,imx);      else if (sum) ii=i; 
       b[i]=sum; 
    for (i=1; i<=imx; i++)    } 
      for(m=2; (m<= maxwav); m++)    for (i=n;i>=1;i--) { 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      sum=b[i]; 
          anint[m][i]=9999;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
          s[m][i]=-1;      b[i]=sum/a[i][i]; 
        }    } 
      } 
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  void pstamp(FILE *fichier)
       for(m=1; (m<= maxwav); m++){  {
         if(s[m][i] >0){    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
           if (s[m][i] == nlstate+1) {  }
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)  /************ Frequencies ********************/
               agev[m][i]=agedc[i];  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
             else {  {  /* Some frequencies */
               if (andc[i]!=9999){    
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    int i, m, jk, j1, bool, z1,j;
               agev[m][i]=-1;    int first;
               }    double ***freq; /* Frequencies */
             }    double *pp, **prop;
           }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           else if(s[m][i] !=9){ /* Should no more exist */    char fileresp[FILENAMELENGTH];
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    
             if(mint[m][i]==99 || anint[m][i]==9999)    pp=vector(1,nlstate);
               agev[m][i]=1;    prop=matrix(1,nlstate,iagemin,iagemax+3);
             else if(agev[m][i] <agemin){    strcpy(fileresp,"p");
               agemin=agev[m][i];    strcat(fileresp,fileres);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    if((ficresp=fopen(fileresp,"w"))==NULL) {
             }      printf("Problem with prevalence resultfile: %s\n", fileresp);
             else if(agev[m][i] >agemax){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
               agemax=agev[m][i];      exit(0);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    }
             }    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
             /*agev[m][i]=anint[m][i]-annais[i];*/    j1=0;
             /*   agev[m][i] = age[i]+2*m;*/    
           }    j=cptcoveff;
           else { /* =9 */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             agev[m][i]=1;  
             s[m][i]=-1;    first=1;
           }  
         }    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
         else /*= 0 Unknown */    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
           agev[m][i]=1;    /*    j1++; */
       }    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
            /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     }          scanf("%d", i);*/
     for (i=1; i<=imx; i++)  {        for (i=-5; i<=nlstate+ndeath; i++)  
       for(m=1; (m<= maxwav); m++){          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         if (s[m][i] > (nlstate+ndeath)) {            for(m=iagemin; m <= iagemax+3; m++)
           printf("Error: Wrong value in nlstate or ndeath\n");                freq[i][jk][m]=0;
           goto end;        
         }        for (i=1; i<=nlstate; i++)  
       }          for(m=iagemin; m <= iagemax+3; m++)
     }            prop[i][m]=0;
         
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        dateintsum=0;
         k2cpt=0;
     free_vector(severity,1,maxwav);        for (i=1; i<=imx; i++) {
     free_imatrix(outcome,1,maxwav+1,1,n);          bool=1;
     free_vector(moisnais,1,n);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
     free_vector(annais,1,n);            for (z1=1; z1<=cptcoveff; z1++)       
     /* free_matrix(mint,1,maxwav,1,n);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
        free_matrix(anint,1,maxwav,1,n);*/                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
     free_vector(moisdc,1,n);                bool=0;
     free_vector(andc,1,n);                /* 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", 
                   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                      j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
     wav=ivector(1,imx);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              } 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          }
       
     /* Concatenates waves */          if (bool==1){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       Tcode=ivector(1,100);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       ncodemax[1]=1;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                if (m<lastpass) {
                        freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    codtab=imatrix(1,100,1,10);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    h=0;                }
    m=pow(2,cptcoveff);                
                  if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
    for(k=1;k<=cptcoveff; k++){                  dateintsum=dateintsum+k2;
      for(i=1; i <=(m/pow(2,k));i++){                  k2cpt++;
        for(j=1; j <= ncodemax[k]; j++){                }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                /*}*/
            h++;            }
            if (h>m) h=1;codtab[h][k]=j;          }
          }        } /* end i */
        }         
      }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
    }        pstamp(ficresp);
         if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
    /*for(i=1; i <=m ;i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      for(k=1; k <=cptcovn; k++){          fprintf(ficresp, "**********\n#");
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          fprintf(ficlog, "\n#********** Variable "); 
      }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      printf("\n");          fprintf(ficlog, "**********\n#");
    }        }
    scanf("%d",i);*/        for(i=1; i<=nlstate;i++) 
              fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
    /* Calculates basic frequencies. Computes observed prevalence at single age        fprintf(ficresp, "\n");
        and prints on file fileres'p'. */        
         for(i=iagemin; i <= iagemax+3; i++){
              if(i==iagemax+3){
                fprintf(ficlog,"Total");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          }else{
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if(first==1){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              first=0;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              printf("See log file for details...\n");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            }
                  fprintf(ficlog,"Age %d", i);
     /* 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] */          for(jk=1; jk <=nlstate ; jk++){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
     if(mle==1){          }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          for(jk=1; jk <=nlstate ; jk++){
     }            for(m=-1, pos=0; m <=0 ; m++)
                  pos += freq[jk][m][i];
     /*--------- results files --------------*/            if(pp[jk]>=1.e-10){
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);              if(first==1){
                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
    jk=1;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    fprintf(ficres,"# Parameters\n");            }else{
    printf("# Parameters\n");              if(first==1)
    for(i=1,jk=1; i <=nlstate; i++){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      for(k=1; k <=(nlstate+ndeath); k++){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
        if (k != i)            }
          {          }
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);          for(jk=1; jk <=nlstate ; jk++){
            for(j=1; j <=ncovmodel; j++){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
              printf("%f ",p[jk]);              pp[jk] += freq[jk][m][i];
              fprintf(ficres,"%f ",p[jk]);          }       
              jk++;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
            }            pos += pp[jk];
            printf("\n");            posprop += prop[jk][i];
            fprintf(ficres,"\n");          }
          }          for(jk=1; jk <=nlstate ; jk++){
      }            if(pos>=1.e-5){
    }              if(first==1)
  if(mle==1){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     /* Computing hessian and covariance matrix */              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     ftolhess=ftol; /* Usually correct */            }else{
     hesscov(matcov, p, npar, delti, ftolhess, func);              if(first==1)
  }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fprintf(ficres,"# Scales\n");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     printf("# Scales\n");            }
      for(i=1,jk=1; i <=nlstate; i++){            if( i <= iagemax){
       for(j=1; j <=nlstate+ndeath; j++){              if(pos>=1.e-5){
         if (j!=i) {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           fprintf(ficres,"%1d%1d",i,j);                /*probs[i][jk][j1]= pp[jk]/pos;*/
           printf("%1d%1d",i,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]);*/
           for(k=1; k<=ncovmodel;k++){              }
             printf(" %.5e",delti[jk]);              else
             fprintf(ficres," %.5e",delti[jk]);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             jk++;            }
           }          }
           printf("\n");          
           fprintf(ficres,"\n");          for(jk=-1; jk <=nlstate+ndeath; jk++)
         }            for(m=-1; m <=nlstate+ndeath; m++)
       }              if(freq[jk][m][i] !=0 ) {
      }              if(first==1)
                    printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     k=1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     fprintf(ficres,"# Covariance\n");              }
     printf("# Covariance\n");          if(i <= iagemax)
     for(i=1;i<=npar;i++){            fprintf(ficresp,"\n");
       /*  if (k>nlstate) k=1;          if(first==1)
       i1=(i-1)/(ncovmodel*nlstate)+1;            printf("Others in log...\n");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          fprintf(ficlog,"\n");
       printf("%s%d%d",alph[k],i1,tab[i]);*/        }
       fprintf(ficres,"%3d",i);        /*}*/
       printf("%3d",i);    }
       for(j=1; j<=i;j++){    dateintmean=dateintsum/k2cpt; 
         fprintf(ficres," %.5e",matcov[i][j]);   
         printf(" %.5e",matcov[i][j]);    fclose(ficresp);
       }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       fprintf(ficres,"\n");    free_vector(pp,1,nlstate);
       printf("\n");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       k++;    /* End of Freq */
     }  }
      
     while((c=getc(ficpar))=='#' && c!= EOF){  /************ Prevalence ********************/
       ungetc(c,ficpar);  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)
       fgets(line, MAXLINE, ficpar);  {  
       puts(line);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       fputs(line,ficparo);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     }       We still use firstpass and lastpass as another selection.
     ungetc(c,ficpar);    */
     
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    int i, m, jk, j1, bool, z1,j;
      
     if (fage <= 2) {    double **prop;
       bage = agemin;    double posprop; 
       fage = agemax;    double  y2; /* in fractional years */
     }    int iagemin, iagemax;
        int first; /** to stop verbosity which is redirected to log file */
     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\n",agemin,agemax,bage,fage);    iagemin= (int) agemin;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    iagemax= (int) agemax;
      /*pp=vector(1,nlstate);*/
     while((c=getc(ficpar))=='#' && c!= EOF){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     ungetc(c,ficpar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     fgets(line, MAXLINE, ficpar);    j1=0;
     puts(line);    
     fputs(line,ficparo);    /*j=cptcoveff;*/
   }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   ungetc(c,ficpar);    
      first=1;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /*for(i1=1; i1<=ncodemax[k1];i1++){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        j1++;*/
              
   while((c=getc(ficpar))=='#' && c!= EOF){        for (i=1; i<=nlstate; i++)  
     ungetc(c,ficpar);          for(m=iagemin; m <= iagemax+3; m++)
     fgets(line, MAXLINE, ficpar);            prop[i][m]=0.0;
     puts(line);       
     fputs(line,ficparo);        for (i=1; i<=imx; i++) { /* Each individual */
   }          bool=1;
   ungetc(c,ficpar);          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                bool=0;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          } 
           if (bool==1) { 
   fscanf(ficpar,"pop_based=%d\n",&popbased);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
    fprintf(ficparo,"pop_based=%d\n",popbased);                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
    fprintf(ficres,"pop_based=%d\n",popbased);                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
   while((c=getc(ficpar))=='#' && c!= EOF){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     ungetc(c,ficpar);                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); 
     fgets(line, MAXLINE, ficpar);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     puts(line);                  /*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]]);*/
     fputs(line,ficparo);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   }                  prop[s[m][i]][iagemax+3] += weight[i]; 
   ungetc(c,ficpar);                } 
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);              }
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            } /* end selection of waves */
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          }
         }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 /*------------ gnuplot -------------*/            posprop += prop[jk][i]; 
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);          } 
            
 /*------------ free_vector  -------------*/          for(jk=1; jk <=nlstate ; jk++){     
  chdir(path);            if( i <=  iagemax){ 
                if(posprop>=1.e-5){ 
  free_ivector(wav,1,imx);                probs[i][jk][j1]= prop[jk][i]/posprop;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              } else{
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                  if(first==1){
  free_ivector(num,1,n);                  first=0;
  free_vector(agedc,1,n);                  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]);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                }
  fclose(ficparo);              }
  fclose(ficres);            } 
            }/* end jk */ 
   /* Reads comments: lines beginning with '#' */        }/* end i */ 
   while((c=getc(ficpar))=='#' && c!= EOF){      /*} *//* end i1 */
     ungetc(c,ficpar);    } /* end j1 */
     fgets(line, MAXLINE, ficpar);    
     puts(line);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     fputs(line,ficparo);    /*free_vector(pp,1,nlstate);*/
   }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   ungetc(c,ficpar);  }  /* End of prevalence */
    
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  /************* Waves Concatenation ***************/
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);  
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  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)
 /*--------- index.htm --------*/  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   /*--------------- Prevalence limit --------------*/       and mw[mi+1][i]. dh depends on stepm.
         */
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);    int i, mi, m;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;       double sum=0., jmean=0.;*/
   }    int first;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    int j, k=0,jk, ju, jl;
   fprintf(ficrespl,"#Prevalence limit\n");    double sum=0.;
   fprintf(ficrespl,"#Age ");    first=0;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    jmin=100000;
   fprintf(ficrespl,"\n");    jmax=-1;
      jmean=0.;
   prlim=matrix(1,nlstate,1,nlstate);    for(i=1; i<=imx; i++){
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      mi=0;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      m=firstpass;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      while(s[m][i] <= nlstate){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          mw[++mi][i]=m;
   k=0;        if(m >=lastpass)
   agebase=agemin;          break;
   agelim=agemax;        else
   ftolpl=1.e-10;          m++;
   i1=cptcoveff;      }/* end while */
   if (cptcovn < 1){i1=1;}      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
   for(cptcov=1;cptcov<=i1;cptcov++){        /* if(mi==0)  never been interviewed correctly before death */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           /* Only death is a correct wave */
         k=k+1;        mw[mi][i]=m;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      }
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)      wav[i]=mi;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      if(mi==0){
         fprintf(ficrespl,"******\n");        nbwarn++;
                if(first==0){
         for (age=agebase; age<=agelim; age++){          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          first=1;
           fprintf(ficrespl,"%.0f",age );        }
           for(i=1; i<=nlstate;i++)        if(first==1){
           fprintf(ficrespl," %.5f", prlim[i][i]);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           fprintf(ficrespl,"\n");        }
         }      } /* end mi==0 */
       }    } /* End individuals */
     }  
   fclose(ficrespl);    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
   /*------------- h Pij x at various ages ------------*/        if (stepm <=0)
            dh[mi][i]=1;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        else{
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            if (agedc[i] < 2*AGESUP) {
   }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   printf("Computing pij: result on file '%s' \n", filerespij);              if(j==0) j=1;  /* Survives at least one month after exam */
                else if(j<0){
   stepsize=(int) (stepm+YEARM-1)/YEARM;                nberr++;
   /*if (stepm<=24) stepsize=2;*/                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Temporary Dangerous patch */
   agelim=AGESUP;                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);
   hstepm=stepsize*YEARM; /* Every year of age */                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]);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                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);
                }
   k=0;              k=k+1;
   for(cptcov=1;cptcov<=i1;cptcov++){              if (j >= jmax){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                jmax=j;
       k=k+1;                ijmax=i;
         fprintf(ficrespij,"\n#****** ");              }
         for(j=1;j<=cptcoveff;j++)              if (j <= jmin){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                jmin=j;
         fprintf(ficrespij,"******\n");                ijmin=i;
                      }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */              sum=sum+j;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           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);            else{
           fprintf(ficrespij,"# Age");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           for(i=1; i<=nlstate;i++)  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);            k=k+1;
           fprintf(ficrespij,"\n");            if (j >= jmax) {
           for (h=0; h<=nhstepm; h++){              jmax=j;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );              ijmax=i;
             for(i=1; i<=nlstate;i++)            }
               for(j=1; j<=nlstate+ndeath;j++)            else if (j <= jmin){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              jmin=j;
             fprintf(ficrespij,"\n");              ijmin=i;
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           fprintf(ficrespij,"\n");            /*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]);*/
         }            if(j<0){
     }              nberr++;
   }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/            }
             sum=sum+j;
   fclose(ficrespij);          }
           jk= j/stepm;
   if(stepm == 1) {          jl= j -jk*stepm;
   /*---------- Forecasting ------------------*/          ju= j -(jk+1)*stepm;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
                dh[mi][i]=jk;
                bh[mi][i]=0;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
   strcpy(fileresf,"f");              bh[mi][i]=ju;
   strcat(fileresf,fileres);            }
   if((ficresf=fopen(fileresf,"w"))==NULL) {          }else{
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;            if(jl <= -ju){
   }              dh[mi][i]=jk;
   printf("Computing forecasting: result on file '%s' \n", fileresf);              bh[mi][i]=jl;       /* bias is positive if real duration
                                     * is higher than the multiple of stepm and negative otherwise.
   free_matrix(mint,1,maxwav,1,n);                                   */
   free_matrix(anint,1,maxwav,1,n);            }
             else{
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   if (mobilav==1) {            }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if(dh[mi][i]==0){
     movingaverage(agedeb, fage, agemin, mobaverage);              dh[mi][i]=1; /* At least one step */
   }              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);*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;            }
   if (stepm<=12) stepsize=1;          } /* end if mle */
          }
   agelim=AGESUP;      } /* end wave */
      }
   hstepm=1;    jmean=sum/k;
   hstepm=hstepm/stepm;    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);
   yp1=modf(dateintmean,&yp);    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);
   anprojmean=yp;   }
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;  /*********** Tricode ****************************/
   yp1=modf((yp2*30.5),&yp);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   jprojmean=yp;  {
   if(jprojmean==0) jprojmean=1;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   if(mprojmean==0) jprojmean=1;    /*      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]
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       * nbcode[Tvar[j]][1]= 
   if (popforecast==1) {    */
     if((ficpop=fopen(popfile,"r"))==NULL)    {  
       printf("Problem with population file : %s\n",popfile);goto end;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     }    int modmaxcovj=0; /* Modality max of covariates j */
     popage=ivector(0,AGESUP);    int cptcode=0; /* Modality max of covariates j */
     popeffectif=vector(0,AGESUP);    int modmincovj=0; /* Modality min of covariates j */
     popcount=vector(0,AGESUP);  
      
     i=1;      cptcoveff=0; 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)   
       {    for (k=-1; k < maxncov; k++) Ndum[k]=0;
         i=i+1;    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
       }  
     imx=i;    /* Loop on covariates without age and products */
        for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   }                                 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
   for(cptcov=1;cptcov<=i1;cptcov++){                                      * If product of Vn*Vm, still boolean *:
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
       k=k+1;                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
       fprintf(ficresf,"\n#******");        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
       for(j=1;j<=cptcoveff;j++) {                                        modality of the nth covariate of individual i. */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if (ij > modmaxcovj)
       }          modmaxcovj=ij; 
       fprintf(ficresf,"******\n");        else if (ij < modmincovj) 
       fprintf(ficresf,"# StartingAge FinalAge");          modmincovj=ij; 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        if ((ij < -1) && (ij > NCOVMAX)){
       if (popforecast==1)  fprintf(ficresf," [Population]");          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
                exit(1);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        }else
         fprintf(ficresf,"\n");        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
                /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        /* getting the maximum value of the modality of the covariate
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
           nhstepm = nhstepm/hstepm;           female is 1, then modmaxcovj=1.*/
                }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
           oldm=oldms;savm=savms;      cptcode=modmaxcovj;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
             /*for (i=0; i<=cptcode; i++) {*/
           for (h=0; h<=nhstepm; h++){      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
             if (h==(int) (calagedate+YEARM*cpt)) {        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
             }          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
               for(i=1; i<=nlstate;i++) {                         historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
                 if (mobilav==1)      } /* Ndum[-1] number of undefined modalities */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
                 }      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
                 if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];         modmincovj=3; modmaxcovj = 7;
               }         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
               if (h==(int)(calagedate+12*cpt)){         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
                 fprintf(ficresf," %.3f", kk1);         variables V1_1 and V1_2.
                       nbcode[Tvar[j]][ij]=k;
                 if (popforecast==1) fprintf(ficresf," [%.f]", kk2);         nbcode[Tvar[j]][1]=0;
               }         nbcode[Tvar[j]][2]=1;
             }         nbcode[Tvar[j]][3]=2;
           }      */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      ij=1; /* ij is similar to i but can jumps over null modalities */
         }      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
       }        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
     }          /*recode from 0 */
   }          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
                    nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                                       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; */
   if (popforecast==1) {            ij++;
     free_ivector(popage,0,AGESUP);          }
     free_vector(popeffectif,0,AGESUP);          if (ij > ncodemax[j]) break; 
     free_vector(popcount,0,AGESUP);        }  /* end of loop on */
   }      } /* end of loop on modality */ 
      } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   free_imatrix(s,1,maxwav+1,1,n);    
   free_vector(weight,1,n);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   fclose(ficresf);    
   }    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   /* End forecasting */     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
   else{     Ndum[ij]++; 
     erreur=108;   } 
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);  
   }   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) */
       /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   /*---------- Health expectancies and variances ------------*/     if((Ndum[i]!=0) && (i<=ncovcol)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   strcpy(filerest,"t");       Tvaraff[ij]=i; /*For printing (unclear) */
   strcat(filerest,fileres);       ij++;
   if((ficrest=fopen(filerest,"w"))==NULL) {     }else
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;         Tvaraff[ij]=0;
   }   }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);   ij--;
    cptcoveff=ij; /*Number of total covariates*/
   
   strcpy(filerese,"e");  }
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  /*********** Health Expectancies ****************/
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
  strcpy(fileresv,"v");  {
   strcat(fileresv,fileres);    /* Health expectancies, no variances */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    int i, j, nhstepm, hstepm, h, nstepm;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    int nhstepma, nstepma; /* Decreasing with age */
   }    double age, agelim, hf;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double ***p3mat;
     double eip;
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    pstamp(ficreseij);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       k=k+1;    fprintf(ficreseij,"# Age");
       fprintf(ficrest,"\n#****** ");    for(i=1; i<=nlstate;i++){
       for(j=1;j<=cptcoveff;j++)      for(j=1; j<=nlstate;j++){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficreseij," e%1d%1d ",i,j);
       fprintf(ficrest,"******\n");      }
       fprintf(ficreseij," e%1d. ",i);
       fprintf(ficreseij,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)    fprintf(ficreseij,"\n");
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    
     if(estepm < stepm){
       fprintf(ficresvij,"\n#****** ");      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    else  hstepm=estepm;   
       fprintf(ficresvij,"******\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     * if stepm=24 months pijx are given only every 2 years and by summing them
       oldm=oldms;savm=savms;     * we are calculating an estimate of the Life Expectancy assuming a linear 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);       * progression in between and thus overestimating or underestimating according
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     * to the curvature of the survival function. If, for the same date, we 
       oldm=oldms;savm=savms;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     * to compare the new estimate of Life expectancy with the same linear 
         * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    /* For example we decided to compute the life expectancy with the smallest unit */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficrest,"\n");       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
       hf=1;       Look at hpijx to understand the reason of that which relies in memory size
       if (stepm >= YEARM) hf=stepm/YEARM;       and note for a fixed period like estepm months */
       epj=vector(1,nlstate+1);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       for(age=bage; age <=fage ;age++){       survival function given by stepm (the optimization length). Unfortunately it
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       means that if the survival funtion is printed only each two years of age and if
         if (popbased==1) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           for(i=1; i<=nlstate;i++)       results. So we changed our mind and took the option of the best precision.
             prlim[i][i]=probs[(int)age][i][k];    */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
          
         fprintf(ficrest," %.0f",age);    agelim=AGESUP;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    /* If stepm=6 months */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           }      
           epj[nlstate+1] +=epj[j];  /* nhstepm age range expressed in number of stepm */
         }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         for(i=1, vepp=0.;i <=nlstate;i++)    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           for(j=1;j <=nlstate;j++)    /* if (stepm >= YEARM) hstepm=1;*/
             vepp += vareij[i][j][(int)age];    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    for (age=bage; age<=fage; age ++){ 
         }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         fprintf(ficrest,"\n");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       }      /* if (stepm >= YEARM) hstepm=1;*/
     }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   }  
              /* If stepm=6 months */
              /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
  fclose(ficreseij);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
  fclose(ficresvij);      
   fclose(ficrest);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   fclose(ficpar);      
   free_vector(epj,1,nlstate+1);      printf("%d|",(int)age);fflush(stdout);
   /*  scanf("%d ",i); */      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        
   /*------- Variance limit prevalence------*/        /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
 strcpy(fileresvpl,"vpl");        for(j=1; j<=nlstate;j++)
   strcat(fileresvpl,fileres);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            
     exit(0);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          }
   
  k=0;      fprintf(ficreseij,"%3.0f",age );
  for(cptcov=1;cptcov<=i1;cptcov++){      for(i=1; i<=nlstate;i++){
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        eip=0;
      k=k+1;        for(j=1; j<=nlstate;j++){
      fprintf(ficresvpl,"\n#****** ");          eip +=eij[i][j][(int)age];
      for(j=1;j<=cptcoveff;j++)          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
      fprintf(ficresvpl,"******\n");        fprintf(ficreseij,"%9.4f", eip );
            }
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      fprintf(ficreseij,"\n");
      oldm=oldms;savm=savms;      
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    }
    }    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  }    printf("\n");
     fprintf(ficlog,"\n");
   fclose(ficresvpl);    
   }
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  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[] )
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  {
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /* Covariances of health expectancies eij and of total life expectancies according
       to initial status i, ei. .
      */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    int nhstepma, nstepma; /* Decreasing with age */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    double age, agelim, hf;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    double ***p3matp, ***p3matm, ***varhe;
      double **dnewm,**doldm;
   free_matrix(matcov,1,npar,1,npar);    double *xp, *xm;
   free_vector(delti,1,npar);    double **gp, **gm;
   free_matrix(agev,1,maxwav,1,imx);    double ***gradg, ***trgradg;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    int theta;
   
   if(erreur >0)    double eip, vip;
     printf("End of Imach with error %d\n",erreur);  
   else   printf("End of Imach\n");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    xp=vector(1,npar);
      xm=vector(1,npar);
   /* 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);*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   /*------ End -----------*/    
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
  end:    fprintf(ficresstdeij,"# Age");
 #ifdef windows    for(i=1; i<=nlstate;i++){
   /* chdir(pathcd);*/      for(j=1; j<=nlstate;j++)
 #endif        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
  /*system("wgnuplot graph.plt");*/      fprintf(ficresstdeij," e%1d. ",i);
  /*system("../gp37mgw/wgnuplot graph.plt");*/    }
  /*system("cd ../gp37mgw");*/    fprintf(ficresstdeij,"\n");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    pstamp(ficrescveij);
  strcat(plotcmd," ");    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
  strcat(plotcmd,optionfilegnuplot);    fprintf(ficrescveij,"# Age");
  system(plotcmd);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
 #ifdef windows        cptj= (j-1)*nlstate+i;
   while (z[0] != 'q') {        for(i2=1; i2<=nlstate;i2++)
     chdir(path);          for(j2=1; j2<=nlstate;j2++){
     printf("\nType e to edit output files, c to start again, and q for exiting: ");            cptj2= (j2-1)*nlstate+i2;
     scanf("%s",z);            if(cptj2 <= cptj)
     if (z[0] == 'c') system("./imach");              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     else if (z[0] == 'e') {          }
       chdir(path);      }
       system(optionfilehtm);    fprintf(ficrescveij,"\n");
     }    
     else if (z[0] == 'q') exit(0);    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
 #endif    }
 }    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         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) */
             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]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     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;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     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);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     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);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     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 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, 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 in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,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 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*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     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*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     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 each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         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]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* 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 ******************/
   void 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, cptcod, i, h, i1;
     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*************/
   void 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];
     int i,j, k, 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 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=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     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 */
       strcpy(line, linetmp);
     
   
       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  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);
   }
   
   int 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 = *nberr + 1;
           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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           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;
                 }
               }
             } /* agedc > 0 */
           }
           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);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
   #if defined(__GNUC__) 
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
   
   #include <stdint.h>
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   /* struct utsname sysInfo;
   
      if (uname(&sysInfo) != -1) {
        printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
             */
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); 
   
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compile for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (ie 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bits windows).\n");
              frintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bits windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   /***********************************************/
   /**************** 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=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *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=0, fage=110, 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 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";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_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.tm_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';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         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("Directory already exists (or can't create it) %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);
   
     syscompilerinfo();
   
     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.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       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");
   #else
       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 */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             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);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     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(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  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");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or 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("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       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.1.26  
changed lines
  Added in v.1.174


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