Diff for /imach/src/imach.c between versions 1.33 and 1.180

version 1.33, 2002/03/12 22:13:38 version 1.180, 2015/02/11 17:33:45
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.180  2015/02/11 17:33:45  brouard
      Summary: Finishing move from main to function (hpijx and prevalence_limit)
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.179  2015/01/04 09:57:06  brouard
   first survey ("cross") where individuals from different ages are    Summary: back to OS/X
   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 1.178  2015/01/04 09:35:48  brouard
   second wave of interviews ("longitudinal") which measure each change    *** empty log message ***
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.177  2015/01/03 18:40:56  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: Still testing ilc32 on OSX
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.176  2015/01/03 16:45:04  brouard
   probabibility to be observed in state j at the second wave    *** empty log message ***
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.175  2015/01/03 16:33:42  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    *** empty log message ***
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.174  2015/01/03 16:15:49  brouard
   you to do it.  More covariates you add, slower the    Summary: Still in cross-compilation
   convergence.  
     Revision 1.173  2015/01/03 12:06:26  brouard
   The advantage of this computer programme, compared to a simple    Summary: trying to detect cross-compilation
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.172  2014/12/27 12:07:47  brouard
   intermediate interview, the information is lost, but taken into    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   account using an interpolation or extrapolation.    
     Revision 1.171  2014/12/23 13:26:59  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: Back from Visual C
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Still problem with utsname.h on Windows
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.170  2014/12/23 11:17:12  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Summary: Cleaning some \%% back to %%
   and the contribution of each individual to the likelihood is simply  
   hPijx.    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.169  2014/12/22 23:08:31  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: 0.98p
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Outputs some informations on compiler used, OS etc. Testing on different platforms.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.168  2014/12/22 15:17:42  brouard
   from the European Union.    Summary: update
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.167  2014/12/22 13:50:56  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Summary: Testing uname and compiler version and if compiled 32 or 64
   **********************************************************************/  
      Testing on Linux 64
 #include <math.h>  
 #include <stdio.h>    Revision 1.166  2014/12/22 11:40:47  brouard
 #include <stdlib.h>    *** empty log message ***
 #include <unistd.h>  
     Revision 1.165  2014/12/16 11:20:36  brouard
 #define MAXLINE 256    Summary: After compiling on Visual C
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    * imach.c (Module): Merging 1.61 to 1.162
 /*#define DEBUG*/  
 #define windows    Revision 1.164  2014/12/16 10:52:11  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     * imach.c (Module): Merging 1.61 to 1.162
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.163  2014/12/16 10:30:11  brouard
     * imach.c (Module): Merging 1.61 to 1.162
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.162  2014/09/25 11:43:39  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Summary: temporary backup 0.99!
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.1  2014/09/16 11:06:58  brouard
 #define YEARM 12. /* Number of months per year */    Summary: With some code (wrong) for nlopt
 #define AGESUP 130  
 #define AGEBASE 40    Author:
   
     Revision 1.161  2014/09/15 20:41:41  brouard
 int erreur; /* Error number */    Summary: Problem with macro SQR on Intel compiler
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.160  2014/09/02 09:24:05  brouard
 int npar=NPARMAX;    *** empty log message ***
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.159  2014/09/01 10:34:10  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Summary: WIN32
 int popbased=0;    Author: Brouard
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.158  2014/08/27 17:11:51  brouard
 int maxwav; /* Maxim number of waves */    *** empty log message ***
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.157  2014/08/27 16:26:55  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Summary: Preparing windows Visual studio version
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Author: Brouard
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    In order to compile on Visual studio, time.h is now correct and time_t
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    and tm struct should be used. difftime should be used but sometimes I
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    just make the differences in raw time format (time(&now).
 FILE *ficgp,*ficresprob,*ficpop;    Trying to suppress #ifdef LINUX
 FILE *ficreseij;    Add xdg-open for __linux in order to open default browser.
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.156  2014/08/25 20:10:10  brouard
   char fileresv[FILENAMELENGTH];    *** empty log message ***
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
 #define NR_END 1    Author: Brouard
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.154  2014/06/20 17:32:08  brouard
     Summary: Outputs now all graphs of convergence to period prevalence
 #define NRANSI  
 #define ITMAX 200    Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
 #define TOL 2.0e-4    Author: Brouard
   
 #define CGOLD 0.3819660    Revision 1.152  2014/06/18 17:54:09  brouard
 #define ZEPS 1.0e-10    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.151  2014/06/18 16:43:30  brouard
 #define GOLD 1.618034    *** empty log message ***
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.150  2014/06/18 16:42:35  brouard
     Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 static double maxarg1,maxarg2;    Author: brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.149  2014/06/18 15:51:14  brouard
      Summary: Some fixes in parameter files errors
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Author: Nicolas Brouard
 #define rint(a) floor(a+0.5)  
     Revision 1.148  2014/06/17 17:38:48  brouard
 static double sqrarg;    Summary: Nothing new
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Author: Brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Just a new packaging for OS/X version 0.98nS
 int imx;  
 int stepm;    Revision 1.147  2014/06/16 10:33:11  brouard
 /* Stepm, step in month: minimum step interpolation*/    *** empty log message ***
   
 int m,nb;    Revision 1.146  2014/06/16 10:20:28  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Summary: Merge
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Author: Brouard
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Merge, before building revised version.
   
 double *weight;    Revision 1.145  2014/06/10 21:23:15  brouard
 int **s; /* Status */    Summary: Debugging with valgrind
 double *agedc, **covar, idx;    Author: Nicolas Brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Lot of changes in order to output the results with some covariates
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    After the Edimburgh REVES conference 2014, it seems mandatory to
 double ftolhess; /* Tolerance for computing hessian */    improve the code.
     No more memory valgrind error but a lot has to be done in order to
 /**************** split *************************/    continue the work of splitting the code into subroutines.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Also, decodemodel has been improved. Tricode is still not
 {    optimal. nbcode should be improved. Documentation has been added in
    char *s;                             /* pointer */    the source code.
    int  l1, l2;                         /* length counters */  
     Revision 1.143  2014/01/26 09:45:38  brouard
    l1 = strlen( path );                 /* length of path */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    s = strrchr( path, '\\' );           /* find last / */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.142  2014/01/26 03:57:36  brouard
 #endif    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
       extern char       *getwd( );  
     Revision 1.141  2014/01/26 02:42:01  brouard
       if ( getwd( dirc ) == NULL ) {    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #else  
       extern char       *getcwd( );    Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.139  2010/06/14 07:50:17  brouard
          return( GLOCK_ERROR_GETCWD );    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
       }    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.138  2010/04/30 18:19:40  brouard
       s++;                              /* after this, the filename */    *** empty log message ***
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.137  2010/04/29 18:11:38  brouard
       strcpy( name, s );                /* save file name */    (Module): Checking covariates for more complex models
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    than V1+V2. A lot of change to be done. Unstable.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.136  2010/04/26 20:30:53  brouard
    l1 = strlen( dirc );                 /* length of directory */    (Module): merging some libgsl code. Fixing computation
 #ifdef windows    of likelione (using inter/intrapolation if mle = 0) in order to
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    get same likelihood as if mle=1.
 #else    Some cleaning of code and comments added.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.135  2009/10/29 15:33:14  brouard
    s = strrchr( name, '.' );            /* find last / */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.134  2009/10/29 13:18:53  brouard
    l1= strlen( name);    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.133  2009/07/06 10:21:25  brouard
    finame[l1-l2]= 0;    just nforces
    return( 0 );                         /* we're done */  
 }    Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
   
 /******************************************/    Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
 void replace(char *s, char*t)  
 {    Revision 1.130  2009/05/26 06:44:34  brouard
   int i;    (Module): Max Covariate is now set to 20 instead of 8. A
   int lg=20;    lot of cleaning with variables initialized to 0. Trying to make
   i=0;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.129  2007/08/31 13:49:27  lievre
     (s[i] = t[i]);    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.128  2006/06/30 13:02:05  brouard
 }    (Module): Clarifications on computing e.j
   
 int nbocc(char *s, char occ)    Revision 1.127  2006/04/28 18:11:50  brouard
 {    (Module): Yes the sum of survivors was wrong since
   int i,j=0;    imach-114 because nhstepm was no more computed in the age
   int lg=20;    loop. Now we define nhstepma in the age loop.
   i=0;    (Module): In order to speed up (in case of numerous covariates) we
   lg=strlen(s);    compute health expectancies (without variances) in a first step
   for(i=0; i<= lg; i++) {    and then all the health expectancies with variances or standard
   if  (s[i] == occ ) j++;    deviation (needs data from the Hessian matrices) which slows the
   }    computation.
   return j;    In the future we should be able to stop the program is only health
 }    expectancies and graph are needed without standard deviations.
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.126  2006/04/28 17:23:28  brouard
 {    (Module): Yes the sum of survivors was wrong since
   int i,lg,j,p=0;    imach-114 because nhstepm was no more computed in the age
   i=0;    loop. Now we define nhstepma in the age loop.
   for(j=0; j<=strlen(t)-1; j++) {    Version 0.98h
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
   lg=strlen(t);    Forecasting file added.
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.124  2006/03/22 17:13:53  lievre
   }    Parameters are printed with %lf instead of %f (more numbers after the comma).
      u[p]='\0';    The log-likelihood is printed in the log file
   
    for(j=0; j<= lg; j++) {    Revision 1.123  2006/03/20 10:52:43  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    * imach.c (Module): <title> changed, corresponds to .htm file
   }    name. <head> headers where missing.
 }  
     * imach.c (Module): Weights can have a decimal point as for
 /********************** nrerror ********************/    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 void nrerror(char error_text[])    Modification of warning when the covariates values are not 0 or
 {    1.
   fprintf(stderr,"ERREUR ...\n");    Version 0.98g
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.122  2006/03/20 09:45:41  brouard
 }    (Module): Weights can have a decimal point as for
 /*********************** vector *******************/    English (a comma might work with a correct LC_NUMERIC environment,
 double *vector(int nl, int nh)    otherwise the weight is truncated).
 {    Modification of warning when the covariates values are not 0 or
   double *v;    1.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Version 0.98g
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.121  2006/03/16 17:45:01  lievre
 }    * imach.c (Module): Comments concerning covariates added
   
 /************************ free vector ******************/    * imach.c (Module): refinements in the computation of lli if
 void free_vector(double*v, int nl, int nh)    status=-2 in order to have more reliable computation if stepm is
 {    not 1 month. Version 0.98f
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 /************************ivector *******************************/    status=-2 in order to have more reliable computation if stepm is
 int *ivector(long nl,long nh)    not 1 month. Version 0.98f
 {  
   int *v;    Revision 1.119  2006/03/15 17:42:26  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): Bug if status = -2, the loglikelihood was
   if (!v) nrerror("allocation failure in ivector");    computed as likelihood omitting the logarithm. Version O.98e
   return v-nl+NR_END;  
 }    Revision 1.118  2006/03/14 18:20:07  brouard
     (Module): varevsij Comments added explaining the second
 /******************free ivector **************************/    table of variances if popbased=1 .
 void free_ivector(int *v, long nl, long nh)    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 {    (Module): Function pstamp added
   free((FREE_ARG)(v+nl-NR_END));    (Module): Version 0.98d
 }  
     Revision 1.117  2006/03/14 17:16:22  brouard
 /******************* imatrix *******************************/    (Module): varevsij Comments added explaining the second
 int **imatrix(long nrl, long nrh, long ncl, long nch)    table of variances if popbased=1 .
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 {    (Module): Function pstamp added
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Module): Version 0.98d
   int **m;  
      Revision 1.116  2006/03/06 10:29:27  brouard
   /* allocate pointers to rows */    (Module): Variance-covariance wrong links and
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    varian-covariance of ej. is needed (Saito).
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.115  2006/02/27 12:17:45  brouard
   m -= nrl;    (Module): One freematrix added in mlikeli! 0.98c
    
      Revision 1.114  2006/02/26 12:57:58  brouard
   /* allocate rows and set pointers to them */    (Module): Some improvements in processing parameter
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    filename with strsep.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.113  2006/02/24 14:20:24  brouard
   m[nrl] -= ncl;    (Module): Memory leaks checks with valgrind and:
      datafile was not closed, some imatrix were not freed and on matrix
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    allocation too.
    
   /* return pointer to array of pointers to rows */    Revision 1.112  2006/01/30 09:55:26  brouard
   return m;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 }  
     Revision 1.111  2006/01/25 20:38:18  brouard
 /****************** free_imatrix *************************/    (Module): Lots of cleaning and bugs added (Gompertz)
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): Comments can be added in data file. Missing date values
       int **m;    can be a simple dot '.'.
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.110  2006/01/25 00:51:50  brouard
 {    (Module): Lots of cleaning and bugs added (Gompertz)
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.109  2006/01/24 19:37:15  brouard
 }    (Module): Comments (lines starting with a #) are allowed in data.
   
 /******************* matrix *******************************/    Revision 1.108  2006/01/19 18:05:42  lievre
 double **matrix(long nrl, long nrh, long ncl, long nch)    Gnuplot problem appeared...
 {    To be fixed
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.106  2006/01/19 13:24:36  brouard
   m += NR_END;    Some cleaning and links added in html output
   m -= nrl;  
     Revision 1.105  2006/01/05 20:23:19  lievre
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    *** empty log message ***
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.104  2005/09/30 16:11:43  lievre
   m[nrl] -= ncl;    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    that the person is alive, then we can code his/her status as -2
   return m;    (instead of missing=-1 in earlier versions) and his/her
 }    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
 /*************************free matrix ************************/    the healthy state at last known wave). Version is 0.98
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.103  2005/09/30 15:54:49  lievre
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    (Module): sump fixed, loop imx fixed, and simplifications.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Revision 1.101  2004/09/15 10:38:38  brouard
 {    Fix on curr_time
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.99  2004/06/05 08:57:40  brouard
   m += NR_END;    *** empty log message ***
   m -= nrl;  
     Revision 1.98  2004/05/16 15:05:56  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    New version 0.97 . First attempt to estimate force of mortality
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    directly from the data i.e. without the need of knowing the health
   m[nrl] += NR_END;    state at each age, but using a Gompertz model: log u =a + b*age .
   m[nrl] -= ncl;    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    The same imach parameter file can be used but the option for mle should be -3.
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Agnès, who wrote this part of the code, tried to keep most of the
   for (j=ncl+1; j<=nch; j++)    former routines in order to include the new code within the former code.
     m[nrl][j]=m[nrl][j-1]+nlay;  
      The output is very simple: only an estimate of the intercept and of
   for (i=nrl+1; i<=nrh; i++) {    the slope with 95% confident intervals.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Current limitations:
       m[i][j]=m[i][j-1]+nlay;    A) Even if you enter covariates, i.e. with the
   }    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   return m;    B) There is no computation of Life Expectancy nor Life Table.
 }  
     Revision 1.97  2004/02/20 13:25:42  lievre
 /*************************free ma3x ************************/    Version 0.96d. Population forecasting command line is (temporarily)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    suppressed.
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Revision 1.96  2003/07/15 15:38:55  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   free((FREE_ARG)(m+nrl-NR_END));    rewritten within the same printf. Workaround: many printfs.
 }  
     Revision 1.95  2003/07/08 07:54:34  brouard
 /***************** f1dim *************************/    * imach.c (Repository):
 extern int ncom;    (Repository): Using imachwizard code to output a more meaningful covariance
 extern double *pcom,*xicom;    matrix (cov(a12,c31) instead of numbers.
 extern double (*nrfunc)(double []);  
      Revision 1.94  2003/06/27 13:00:02  brouard
 double f1dim(double x)    Just cleaning
 {  
   int j;    Revision 1.93  2003/06/25 16:33:55  brouard
   double f;    (Module): On windows (cygwin) function asctime_r doesn't
   double *xt;    exist so I changed back to asctime which exists.
      (Module): Version 0.96b
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Revision 1.92  2003/06/25 16:30:45  brouard
   f=(*nrfunc)(xt);    (Module): On windows (cygwin) function asctime_r doesn't
   free_vector(xt,1,ncom);    exist so I changed back to asctime which exists.
   return f;  
 }    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
 /*****************brent *************************/    (Repository): Elapsed time after each iteration is now output. It
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    helps to forecast when convergence will be reached. Elapsed time
 {    is stamped in powell.  We created a new html file for the graphs
   int iter;    concerning matrix of covariance. It has extension -cov.htm.
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    Revision 1.90  2003/06/24 12:34:15  brouard
   double ftemp;    (Module): Some bugs corrected for windows. Also, when
   double p,q,r,tol1,tol2,u,v,w,x,xm;    mle=-1 a template is output in file "or"mypar.txt with the design
   double e=0.0;    of the covariance matrix to be input.
    
   a=(ax < cx ? ax : cx);    Revision 1.89  2003/06/24 12:30:52  brouard
   b=(ax > cx ? ax : cx);    (Module): Some bugs corrected for windows. Also, when
   x=w=v=bx;    mle=-1 a template is output in file "or"mypar.txt with the design
   fw=fv=fx=(*f)(x);    of the covariance matrix to be input.
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    Revision 1.88  2003/06/23 17:54:56  brouard
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    Revision 1.87  2003/06/18 12:26:01  brouard
 #ifdef DEBUG    Version 0.96
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    Revision 1.86  2003/06/17 20:04:08  brouard
 #endif    (Module): Change position of html and gnuplot routines and added
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    routine fileappend.
       *xmin=x;  
       return fx;    Revision 1.85  2003/06/17 13:12:43  brouard
     }    * imach.c (Repository): Check when date of death was earlier that
     ftemp=fu;    current date of interview. It may happen when the death was just
     if (fabs(e) > tol1) {    prior to the death. In this case, dh was negative and likelihood
       r=(x-w)*(fx-fv);    was wrong (infinity). We still send an "Error" but patch by
       q=(x-v)*(fx-fw);    assuming that the date of death was just one stepm after the
       p=(x-v)*q-(x-w)*r;    interview.
       q=2.0*(q-r);    (Repository): Because some people have very long ID (first column)
       if (q > 0.0) p = -p;    we changed int to long in num[] and we added a new lvector for
       q=fabs(q);    memory allocation. But we also truncated to 8 characters (left
       etemp=e;    truncation)
       e=d;    (Repository): No more line truncation errors.
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    Revision 1.84  2003/06/13 21:44:43  brouard
       else {    * imach.c (Repository): Replace "freqsummary" at a correct
         d=p/q;    place. It differs from routine "prevalence" which may be called
         u=x+d;    many times. Probs is memory consuming and must be used with
         if (u-a < tol2 || b-u < tol2)    parcimony.
           d=SIGN(tol1,xm-x);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       }  
     } else {    Revision 1.83  2003/06/10 13:39:11  lievre
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    *** empty log message ***
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    Revision 1.82  2003/06/05 15:57:20  brouard
     fu=(*f)(u);    Add log in  imach.c and  fullversion number is now printed.
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  */
       SHFT(v,w,x,u)  /*
         SHFT(fv,fw,fx,fu)     Interpolated Markov Chain
         } else {  
           if (u < x) a=u; else b=u;    Short summary of the programme:
           if (fu <= fw || w == x) {    
             v=w;    This program computes Healthy Life Expectancies from
             w=u;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
             fv=fw;    first survey ("cross") where individuals from different ages are
             fw=fu;    interviewed on their health status or degree of disability (in the
           } else if (fu <= fv || v == x || v == w) {    case of a health survey which is our main interest) -2- at least a
             v=u;    second wave of interviews ("longitudinal") which measure each change
             fv=fu;    (if any) in individual health status.  Health expectancies are
           }    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
   }    Maximum Likelihood of the parameters involved in the model.  The
   nrerror("Too many iterations in brent");    simplest model is the multinomial logistic model where pij is the
   *xmin=x;    probability to be observed in state j at the second wave
   return fx;    conditional to be observed in state i at the first wave. Therefore
 }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
 /****************** mnbrak ***********************/    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    you to do it.  More covariates you add, slower the
             double (*func)(double))    convergence.
 {  
   double ulim,u,r,q, dum;    The advantage of this computer programme, compared to a simple
   double fu;    multinomial logistic model, is clear when the delay between waves is not
      identical for each individual. Also, if a individual missed an
   *fa=(*func)(*ax);    intermediate interview, the information is lost, but taken into
   *fb=(*func)(*bx);    account using an interpolation or extrapolation.  
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)    hPijx is the probability to be observed in state i at age x+h
       SHFT(dum,*fb,*fa,dum)    conditional to the observed state i at age x. The delay 'h' can be
       }    split into an exact number (nh*stepm) of unobserved intermediate
   *cx=(*bx)+GOLD*(*bx-*ax);    states. This elementary transition (by month, quarter,
   *fc=(*func)(*cx);    semester or year) is modelled as a multinomial logistic.  The hPx
   while (*fb > *fc) {    matrix is simply the matrix product of nh*stepm elementary matrices
     r=(*bx-*ax)*(*fb-*fc);    and the contribution of each individual to the likelihood is simply
     q=(*bx-*cx)*(*fb-*fa);    hPijx.
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    Also this programme outputs the covariance matrix of the parameters but also
     ulim=(*bx)+GLIMIT*(*cx-*bx);    of the life expectancies. It also computes the period (stable) prevalence. 
     if ((*bx-u)*(u-*cx) > 0.0) {    
       fu=(*func)(u);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     } else if ((*cx-u)*(u-ulim) > 0.0) {             Institut national d'études démographiques, Paris.
       fu=(*func)(u);    This software have been partly granted by Euro-REVES, a concerted action
       if (fu < *fc) {    from the European Union.
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    It is copyrighted identically to a GNU software product, ie programme and
           SHFT(*fb,*fc,fu,(*func)(u))    software can be distributed freely for non commercial use. Latest version
           }    can be accessed at http://euroreves.ined.fr/imach .
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       fu=(*func)(u);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     } else {    
       u=(*cx)+GOLD*(*cx-*bx);    **********************************************************************/
       fu=(*func)(u);  /*
     }    main
     SHFT(*ax,*bx,*cx,u)    read parameterfile
       SHFT(*fa,*fb,*fc,fu)    read datafile
       }    concatwav
 }    freqsummary
     if (mle >= 1)
 /*************** linmin ************************/      mlikeli
     print results files
 int ncom;    if mle==1 
 double *pcom,*xicom;       computes hessian
 double (*nrfunc)(double []);    read end of parameter file: agemin, agemax, bage, fage, estepm
          begin-prev-date,...
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    open gnuplot file
 {    open html file
   double brent(double ax, double bx, double cx,    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
                double (*f)(double), double tol, double *xmin);     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   double f1dim(double x);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      freexexit2 possible for memory heap.
               double *fc, double (*func)(double));  
   int j;    h Pij x                         | pij_nom  ficrestpij
   double xx,xmin,bx,ax;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   double fx,fb,fa;         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
   ncom=n;  
   pcom=vector(1,n);         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   xicom=vector(1,n);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   nrfunc=func;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   for (j=1;j<=n;j++) {     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
     pcom[j]=p[j];     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
     xicom[j]=xi[j];  
   }    forecasting if prevfcast==1 prevforecast call prevalence()
   ax=0.0;    health expectancies
   xx=1.0;    Variance-covariance of DFLE
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    prevalence()
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);     movingaverage()
 #ifdef DEBUG    varevsij() 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    if popbased==1 varevsij(,popbased)
 #endif    total life expectancies
   for (j=1;j<=n;j++) {    Variance of period (stable) prevalence
     xi[j] *= xmin;   end
     p[j] += xi[j];  */
   }  
   free_vector(xicom,1,n);  #define POWELL /* Instead of NLOPT */
   free_vector(pcom,1,n);  
 }  #include <math.h>
   #include <stdio.h>
 /*************** powell ************************/  #include <stdlib.h>
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #include <string.h>
             double (*func)(double []))  
 {  #ifdef _WIN32
   void linmin(double p[], double xi[], int n, double *fret,  #include <io.h>
               double (*func)(double []));  #include <windows.h>
   int i,ibig,j;  #include <tchar.h>
   double del,t,*pt,*ptt,*xit;  #else
   double fp,fptt;  #include <unistd.h>
   double *xits;  #endif
   pt=vector(1,n);  
   ptt=vector(1,n);  #include <limits.h>
   xit=vector(1,n);  #include <sys/types.h>
   xits=vector(1,n);  
   *fret=(*func)(p);  #if defined(__GNUC__)
   for (j=1;j<=n;j++) pt[j]=p[j];  #include <sys/utsname.h> /* Doesn't work on Windows */
   for (*iter=1;;++(*iter)) {  #endif
     fp=(*fret);  
     ibig=0;  #include <sys/stat.h>
     del=0.0;  #include <errno.h>
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /* extern int errno; */
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  /* #ifdef LINUX */
     printf("\n");  /* #include <time.h> */
     for (i=1;i<=n;i++) {  /* #include "timeval.h" */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /* #else */
       fptt=(*fret);  /* #include <sys/time.h> */
 #ifdef DEBUG  /* #endif */
       printf("fret=%lf \n",*fret);  
 #endif  #include <time.h>
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  #ifdef GSL
       if (fabs(fptt-(*fret)) > del) {  #include <gsl/gsl_errno.h>
         del=fabs(fptt-(*fret));  #include <gsl/gsl_multimin.h>
         ibig=i;  #endif
       }  
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  #ifdef NLOPT
       for (j=1;j<=n;j++) {  #include <nlopt.h>
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  typedef struct {
         printf(" x(%d)=%.12e",j,xit[j]);    double (* function)(double [] );
       }  } myfunc_data ;
       for(j=1;j<=n;j++)  #endif
         printf(" p=%.12e",p[j]);  
       printf("\n");  /* #include <libintl.h> */
 #endif  /* #define _(String) gettext (String) */
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
 #ifdef DEBUG  
       int k[2],l;  #define GNUPLOTPROGRAM "gnuplot"
       k[0]=1;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       k[1]=-1;  #define FILENAMELENGTH 132
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
         printf(" %.12e",p[j]);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       printf("\n");  
       for(l=0;l<=1;l++) {  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         for (j=1;j<=n;j++) {  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #define NINTERVMAX 8
         }  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       }  #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
   #define YEARM 12. /**< Number of months per year */
       free_vector(xit,1,n);  #define AGESUP 130
       free_vector(xits,1,n);  #define AGEBASE 40
       free_vector(ptt,1,n);  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
       free_vector(pt,1,n);  #ifdef _WIN32
       return;  #define DIRSEPARATOR '\\'
     }  #define CHARSEPARATOR "\\"
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define ODIRSEPARATOR '/'
     for (j=1;j<=n;j++) {  #else
       ptt[j]=2.0*p[j]-pt[j];  #define DIRSEPARATOR '/'
       xit[j]=p[j]-pt[j];  #define CHARSEPARATOR "/"
       pt[j]=p[j];  #define ODIRSEPARATOR '\\'
     }  #endif
     fptt=(*func)(ptt);  
     if (fptt < fp) {  /* $Id$ */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /* $State$ */
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  char version[]="Imach version 0.98p, Février 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
         for (j=1;j<=n;j++) {  char fullversion[]="$Revision$ $Date$"; 
           xi[j][ibig]=xi[j][n];  char strstart[80];
           xi[j][n]=xit[j];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
         }  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 #ifdef DEBUG  int nvar=0, nforce=0; /* Number of variables, number of forces */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
         for(j=1;j<=n;j++)  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
           printf(" %.12e",xit[j]);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
         printf("\n");  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
 #endif  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       }  int cptcovprodnoage=0; /**< Number of covariate products without age */   
     }  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   }  int cptcov=0; /* Working variable */
 }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 /**** Prevalence limit ****************/  int ndeath=1; /* Number of dead states */
   int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int popbased=0;
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int *wav; /* Number of waves for this individuual 0 is possible */
      matrix by transitions matrix until convergence is reached */  int maxwav=0; /* Maxim number of waves */
   int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   int i, ii,j,k;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   double min, max, maxmin, maxmax,sumnew=0.;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   double **matprod2();                     to the likelihood and the sum of weights (done by funcone)*/
   double **out, cov[NCOVMAX], **pmij();  int mle=1, weightopt=0;
   double **newm;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double agefin, delaymax=50 ; /* Max number of years to converge */  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
   for (ii=1;ii<=nlstate+ndeath;ii++)             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     for (j=1;j<=nlstate+ndeath;j++){  int countcallfunc=0;  /* Count the number of calls to func */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double jmean=1; /* Mean space between 2 waves */
     }  double **matprod2(); /* test */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
    cov[1]=1.;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    /*FILE *fic ; */ /* Used in readdata only */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  FILE *ficlog, *ficrespow;
     newm=savm;  int globpr=0; /* Global variable for printing or not */
     /* Covariates have to be included here again */  double fretone; /* Only one call to likelihood */
      cov[2]=agefin;  long ipmx=0; /* Number of contributions */
    double sw; /* Sum of weights */
       for (k=1; k<=cptcovn;k++) {  char filerespow[FILENAMELENGTH];
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  FILE *ficresilk;
       }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       for (k=1; k<=cptcovage;k++)  FILE *ficresprobmorprev;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  FILE *fichtm, *fichtmcov; /* Html File */
       for (k=1; k<=cptcovprod;k++)  FILE *ficreseij;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  char fileresstde[FILENAMELENGTH];
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
     savm=oldm;  FILE  *ficresvpl;
     oldm=newm;  char fileresvpl[FILENAMELENGTH];
     maxmax=0.;  char title[MAXLINE];
     for(j=1;j<=nlstate;j++){  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       min=1.;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       max=0.;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       for(i=1; i<=nlstate; i++) {  char command[FILENAMELENGTH];
         sumnew=0;  int  outcmd=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
       maxmin=max-min;  char fileregp[FILENAMELENGTH];
       maxmax=FMAX(maxmax,maxmin);  char popfile[FILENAMELENGTH];
     }  
     if(maxmax < ftolpl){  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       return prlim;  
     }  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
   }  /* struct timezone tzp; */
 }  /* extern int gettimeofday(); */
   struct tm tml, *gmtime(), *localtime();
 /*************** transition probabilities ***************/  
   extern time_t time();
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   double s1, s2;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   /*double t34;*/  struct tm tm;
   int i,j,j1, nc, ii, jj;  
   char strcurr[80], strfor[80];
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  char *endptr;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  long lval;
         /*s2 += param[i][j][nc]*cov[nc];*/  double dval;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  #define NR_END 1
       }  #define FREE_ARG char*
       ps[i][j]=s2;  #define FTOL 1.0e-10
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  #define NRANSI 
     for(j=i+1; j<=nlstate+ndeath;j++){  #define ITMAX 200 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define TOL 2.0e-4 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  #define CGOLD 0.3819660 
       ps[i][j]=s2;  #define ZEPS 1.0e-10 
     }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   }  
     /*ps[3][2]=1;*/  #define GOLD 1.618034 
   #define GLIMIT 100.0 
   for(i=1; i<= nlstate; i++){  #define TINY 1.0e-20 
      s1=0;  
     for(j=1; j<i; j++)  static double maxarg1,maxarg2;
       s1+=exp(ps[i][j]);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     for(j=i+1; j<=nlstate+ndeath; j++)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       s1+=exp(ps[i][j]);    
     ps[i][i]=1./(s1+1.);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     for(j=1; j<i; j++)  #define rint(a) floor(a+0.5)
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
     for(j=i+1; j<=nlstate+ndeath; j++)  /* #define mytinydouble 1.0e-16 */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   } /* end i */  /* static double dsqrarg; */
   /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  static double sqrarg;
     for(jj=1; jj<= nlstate+ndeath; jj++){  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       ps[ii][jj]=0;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       ps[ii][ii]=1;  int agegomp= AGEGOMP;
     }  
   }  int imx; 
   int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  int estepm;
      printf("%lf ",ps[ii][jj]);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    }  
     printf("\n ");  int m,nb;
     }  long *num;
     printf("\n ");printf("%lf ",cov[2]);*/  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 /*  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  double **pmmij, ***probs;
   goto end;*/  double *ageexmed,*agecens;
     return ps;  double dateintmean=0;
 }  
   double *weight;
 /**************** Product of 2 matrices ******************/  int **s; /* Status */
   double *agedc;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
 {                    * covar=matrix(0,NCOVMAX,1,n); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  double  idx; 
   /* in, b, out are matrice of pointers which should have been initialized  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
      before: only the contents of out is modified. The function returns  int *Ndum; /** Freq of modality (tricode */
      a pointer to pointers identical to out */  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   long i, j, k;  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   for(i=nrl; i<= nrh; i++)  double *lsurv, *lpop, *tpop;
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
         out[i][k] +=in[i][j]*b[j][k];  double ftolhess; /**< Tolerance for computing hessian */
   
   return out;  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
     /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 /************* Higher Matrix Product ***************/       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    char  *ss;                            /* pointer */
 {    int   l1, l2;                         /* length counters */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until    l1 = strlen(path );                   /* length of path */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      (typically every 2 years instead of every month which is too big).    if ( ss == NULL ) {                   /* no directory, so determine current directory */
      Model is determined by parameters x and covariates have to be      strcpy( name, path );               /* we got the fullname name because no directory */
      included manually here.      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      */      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
   int i, j, d, h, k;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   double **out, cov[NCOVMAX];        return( GLOCK_ERROR_GETCWD );
   double **newm;      }
       /* got dirc from getcwd*/
   /* Hstepm could be zero and should return the unit matrix */      printf(" DIRC = %s \n",dirc);
   for (i=1;i<=nlstate+ndeath;i++)    } else {                              /* strip direcotry from path */
     for (j=1;j<=nlstate+ndeath;j++){      ss++;                               /* after this, the filename */
       oldm[i][j]=(i==j ? 1.0 : 0.0);      l2 = strlen( ss );                  /* length of filename */
       po[i][j][0]=(i==j ? 1.0 : 0.0);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     }      strcpy( name, ss );         /* save file name */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   for(h=1; h <=nhstepm; h++){      dirc[l1-l2] = 0;                    /* add zero */
     for(d=1; d <=hstepm; d++){      printf(" DIRC2 = %s \n",dirc);
       newm=savm;    }
       /* Covariates have to be included here again */    /* We add a separator at the end of dirc if not exists */
       cov[1]=1.;    l1 = strlen( dirc );                  /* length of directory */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    if( dirc[l1-1] != DIRSEPARATOR ){
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      dirc[l1] =  DIRSEPARATOR;
       for (k=1; k<=cptcovage;k++)      dirc[l1+1] = 0; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      printf(" DIRC3 = %s \n",dirc);
       for (k=1; k<=cptcovprod;k++)    }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
       ss++;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      strcpy(ext,ss);                     /* save extension */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      l1= strlen( name);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      l2= strlen(ss)+1;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      strncpy( finame, name, l1-l2);
       savm=oldm;      finame[l1-l2]= 0;
       oldm=newm;    }
     }  
     for(i=1; i<=nlstate+ndeath; i++)    return( 0 );                          /* we're done */
       for(j=1;j<=nlstate+ndeath;j++) {  }
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  /******************************************/
       }  
   } /* end h */  void replace_back_to_slash(char *s, char*t)
   return po;  {
 }    int i;
     int lg=0;
     i=0;
 /*************** log-likelihood *************/    lg=strlen(t);
 double func( double *x)    for(i=0; i<= lg; i++) {
 {      (s[i] = t[i]);
   int i, ii, j, k, mi, d, kk;      if (t[i]== '\\') s[i]='/';
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    }
   double **out;  }
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  char *trimbb(char *out, char *in)
   long ipmx;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   /*extern weight */    char *s;
   /* We are differentiating ll according to initial status */    s=out;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    while (*in != '\0'){
   /*for(i=1;i<imx;i++)      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     printf(" %d\n",s[4][i]);        in++;
   */      }
   cov[1]=1.;      *out++ = *in++;
     }
   for(k=1; k<=nlstate; k++) ll[k]=0.;    *out='\0';
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    return s;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  }
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  char *cutl(char *blocc, char *alocc, char *in, char occ)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
       for(d=0; d<dh[mi][i]; d++){    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
         newm=savm;       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;       gives blocc="abcdef2ghi" and alocc="j".
         for (kk=1; kk<=cptcovage;kk++) {       If occ is not found blocc is null and alocc is equal to in. Returns blocc
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    */
         }    char *s, *t;
            t=in;s=in;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    while ((*in != occ) && (*in != '\0')){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      *alocc++ = *in++;
         savm=oldm;    }
         oldm=newm;    if( *in == occ){
              *(alocc)='\0';
              s=++in;
       } /* end mult */    }
         
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    if (s == t) {/* occ not found */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      *(alocc-(in-s))='\0';
       ipmx +=1;      in=s;
       sw += weight[i];    }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    while ( *in != '\0'){
     } /* end of wave */      *blocc++ = *in++;
   } /* end of individual */    }
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    *blocc='\0';
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    return t;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  }
   return -l;  char *cutv(char *blocc, char *alocc, char *in, char occ)
 }  {
     /* 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')
 /*********** Maximum Likelihood Estimation ***************/       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    */
 {    char *s, *t;
   int i,j, iter;    t=in;s=in;
   double **xi,*delti;    while (*in != '\0'){
   double fret;      while( *in == occ){
   xi=matrix(1,npar,1,npar);        *blocc++ = *in++;
   for (i=1;i<=npar;i++)        s=in;
     for (j=1;j<=npar;j++)      }
       xi[i][j]=(i==j ? 1.0 : 0.0);      *blocc++ = *in++;
   printf("Powell\n");    }
   powell(p,xi,npar,ftol,&iter,&fret,func);    if (s == t) /* occ not found */
       *(blocc-(in-s))='\0';
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    else
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      *(blocc-(in-s)-1)='\0';
     in=s;
 }    while ( *in != '\0'){
       *alocc++ = *in++;
 /**** Computes Hessian and covariance matrix ***/    }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {    *alocc='\0';
   double  **a,**y,*x,pd;    return s;
   double **hess;  }
   int i, j,jk;  
   int *indx;  int nbocc(char *s, char occ)
   {
   double hessii(double p[], double delta, int theta, double delti[]);    int i,j=0;
   double hessij(double p[], double delti[], int i, int j);    int lg=20;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    i=0;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    lg=strlen(s);
     for(i=0; i<= lg; i++) {
   hess=matrix(1,npar,1,npar);    if  (s[i] == occ ) j++;
     }
   printf("\nCalculation of the hessian matrix. Wait...\n");    return j;
   for (i=1;i<=npar;i++){  }
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /* void cutv(char *u,char *v, char*t, char occ) */
     /*printf(" %f ",p[i]);*/  /* { */
     /*printf(" %lf ",hess[i][i]);*/  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
    /*      gives u="abcdef2ghi" and v="j" *\/ */
   for (i=1;i<=npar;i++) {  /*   int i,lg,j,p=0; */
     for (j=1;j<=npar;j++)  {  /*   i=0; */
       if (j>i) {  /*   lg=strlen(t); */
         printf(".%d%d",i,j);fflush(stdout);  /*   for(j=0; j<=lg-1; j++) { */
         hess[i][j]=hessij(p,delti,i,j);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
         hess[j][i]=hess[i][j];      /*   } */
         /*printf(" %lf ",hess[i][j]);*/  
       }  /*   for(j=0; j<p; j++) { */
     }  /*     (u[j] = t[j]); */
   }  /*   } */
   printf("\n");  /*      u[p]='\0'; */
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /*    for(j=0; j<= lg; j++) { */
    /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   a=matrix(1,npar,1,npar);  /*   } */
   y=matrix(1,npar,1,npar);  /* } */
   x=vector(1,npar);  
   indx=ivector(1,npar);  #ifdef _WIN32
   for (i=1;i<=npar;i++)  char * strsep(char **pp, const char *delim)
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  {
   ludcmp(a,npar,indx,&pd);    char *p, *q;
            
   for (j=1;j<=npar;j++) {    if ((p = *pp) == NULL)
     for (i=1;i<=npar;i++) x[i]=0;      return 0;
     x[j]=1;    if ((q = strpbrk (p, delim)) != NULL)
     lubksb(a,npar,indx,x);    {
     for (i=1;i<=npar;i++){      *pp = q + 1;
       matcov[i][j]=x[i];      *q = '\0';
     }    }
   }    else
       *pp = 0;
   printf("\n#Hessian matrix#\n");    return p;
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++) {  #endif
       printf("%.3e ",hess[i][j]);  
     }  /********************** nrerror ********************/
     printf("\n");  
   }  void nrerror(char error_text[])
   {
   /* Recompute Inverse */    fprintf(stderr,"ERREUR ...\n");
   for (i=1;i<=npar;i++)    fprintf(stderr,"%s\n",error_text);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    exit(EXIT_FAILURE);
   ludcmp(a,npar,indx,&pd);  }
   /*********************** vector *******************/
   /*  printf("\n#Hessian matrix recomputed#\n");  double *vector(int nl, int nh)
   {
   for (j=1;j<=npar;j++) {    double *v;
     for (i=1;i<=npar;i++) x[i]=0;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     x[j]=1;    if (!v) nrerror("allocation failure in vector");
     lubksb(a,npar,indx,x);    return v-nl+NR_END;
     for (i=1;i<=npar;i++){  }
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);  /************************ free vector ******************/
     }  void free_vector(double*v, int nl, int nh)
     printf("\n");  {
   }    free((FREE_ARG)(v+nl-NR_END));
   */  }
   
   free_matrix(a,1,npar,1,npar);  /************************ivector *******************************/
   free_matrix(y,1,npar,1,npar);  int *ivector(long nl,long nh)
   free_vector(x,1,npar);  {
   free_ivector(indx,1,npar);    int *v;
   free_matrix(hess,1,npar,1,npar);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 }  }
   
 /*************** hessian matrix ****************/  /******************free ivector **************************/
 double hessii( double x[], double delta, int theta, double delti[])  void free_ivector(int *v, long nl, long nh)
 {  {
   int i;    free((FREE_ARG)(v+nl-NR_END));
   int l=1, lmax=20;  }
   double k1,k2;  
   double p2[NPARMAX+1];  /************************lvector *******************************/
   double res;  long *lvector(long nl,long nh)
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  {
   double fx;    long *v;
   int k=0,kmax=10;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   double l1;    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   fx=func(x);  }
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){  /******************free lvector **************************/
     l1=pow(10,l);  void free_lvector(long *v, long nl, long nh)
     delts=delt;  {
     for(k=1 ; k <kmax; k=k+1){    free((FREE_ARG)(v+nl-NR_END));
       delt = delta*(l1*k);  }
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  /******************* imatrix *******************************/
       p2[theta]=x[theta]-delt;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       k2=func(p2)-fx;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       /*res= (k1-2.0*fx+k2)/delt/delt; */  { 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
          int **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);    /* allocate pointers to rows */ 
 #endif    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    if (!m) nrerror("allocation failure 1 in matrix()"); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    m += NR_END; 
         k=kmax;    m -= nrl; 
       }    
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    
         k=kmax; l=lmax*10.;    /* allocate rows and set pointers to them */ 
       }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         delts=delt;    m[nrl] += NR_END; 
       }    m[nrl] -= ncl; 
     }    
   }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   delti[theta]=delts;    
   return res;    /* return pointer to array of pointers to rows */ 
      return m; 
 }  } 
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  /****************** free_imatrix *************************/
 {  void free_imatrix(m,nrl,nrh,ncl,nch)
   int i;        int **m;
   int l=1, l1, lmax=20;        long nch,ncl,nrh,nrl; 
   double k1,k2,k3,k4,res,fx;       /* free an int matrix allocated by imatrix() */ 
   double p2[NPARMAX+1];  { 
   int k;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
   fx=func(x);  } 
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  /******************* matrix *******************************/
     p2[thetai]=x[thetai]+delti[thetai]/k;  double **matrix(long nrl, long nrh, long ncl, long nch)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  {
     k1=func(p2)-fx;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      double **m;
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     k2=func(p2)-fx;    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
     p2[thetai]=x[thetai]-delti[thetai]/k;    m -= nrl;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     p2[thetai]=x[thetai]-delti[thetai]/k;    m[nrl] += NR_END;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    m[nrl] -= ncl;
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 #ifdef DEBUG    return 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);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
 #endif  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   }  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   return res;     */
 }  }
   
 /************** Inverse of matrix **************/  /*************************free matrix ************************/
 void ludcmp(double **a, int n, int *indx, double *d)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 {  {
   int i,imax,j,k;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double big,dum,sum,temp;    free((FREE_ARG)(m+nrl-NR_END));
   double *vv;  }
    
   vv=vector(1,n);  /******************* ma3x *******************************/
   *d=1.0;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (i=1;i<=n;i++) {  {
     big=0.0;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     for (j=1;j<=n;j++)    double ***m;
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     vv[i]=1.0/big;    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
   for (j=1;j<=n;j++) {    m -= nrl;
     for (i=1;i<j;i++) {  
       sum=a[i][j];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       a[i][j]=sum;    m[nrl] += NR_END;
     }    m[nrl] -= ncl;
     big=0.0;  
     for (i=j;i<=n;i++) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       sum=a[i][j];  
       for (k=1;k<j;k++)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         sum -= a[i][k]*a[k][j];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       a[i][j]=sum;    m[nrl][ncl] += NR_END;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    m[nrl][ncl] -= nll;
         big=dum;    for (j=ncl+1; j<=nch; j++) 
         imax=i;      m[nrl][j]=m[nrl][j-1]+nlay;
       }    
     }    for (i=nrl+1; i<=nrh; i++) {
     if (j != imax) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (k=1;k<=n;k++) {      for (j=ncl+1; j<=nch; j++) 
         dum=a[imax][k];        m[i][j]=m[i][j-1]+nlay;
         a[imax][k]=a[j][k];    }
         a[j][k]=dum;    return m; 
       }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       *d = -(*d);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       vv[imax]=vv[j];    */
     }  }
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  /*************************free ma3x ************************/
     if (j != n) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       dum=1.0/(a[j][j]);  {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   }    free((FREE_ARG)(m+nrl-NR_END));
   free_vector(vv,1,n);  /* Doesn't work */  }
 ;  
 }  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
 void lubksb(double **a, int n, int *indx, double b[])  {
 {    /* Caution optionfilefiname is hidden */
   int i,ii=0,ip,j;    strcpy(tmpout,optionfilefiname);
   double sum;    strcat(tmpout,"/"); /* Add to the right */
      strcat(tmpout,fileres);
   for (i=1;i<=n;i++) {    return tmpout;
     ip=indx[i];  }
     sum=b[ip];  
     b[ip]=b[i];  /*************** function subdirf2 ***********/
     if (ii)  char *subdirf2(char fileres[], char *preop)
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  {
     else if (sum) ii=i;    
     b[i]=sum;    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
   for (i=n;i>=1;i--) {    strcat(tmpout,"/");
     sum=b[i];    strcat(tmpout,preop);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    strcat(tmpout,fileres);
     b[i]=sum/a[i][i];    return tmpout;
   }  }
 }  
   /*************** function subdirf3 ***********/
 /************ Frequencies ********************/  char *subdirf3(char fileres[], char *preop, char *preop2)
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  {
 {  /* Some frequencies */    
      /* Caution optionfilefiname is hidden */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    strcpy(tmpout,optionfilefiname);
   double ***freq; /* Frequencies */    strcat(tmpout,"/");
   double *pp;    strcat(tmpout,preop);
   double pos, k2, dateintsum=0,k2cpt=0;    strcat(tmpout,preop2);
   FILE *ficresp;    strcat(tmpout,fileres);
   char fileresp[FILENAMELENGTH];    return tmpout;
    }
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  char *asc_diff_time(long time_sec, char ascdiff[])
   strcpy(fileresp,"p");  {
   strcat(fileresp,fileres);    long sec_left, days, hours, minutes;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    days = (time_sec) / (60*60*24);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    sec_left = (time_sec) % (60*60*24);
     exit(0);    hours = (sec_left) / (60*60) ;
   }    sec_left = (sec_left) %(60*60);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    minutes = (sec_left) /60;
   j1=0;    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   j=cptcoveff;    return ascdiff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
   
   for(k1=1; k1<=j;k1++){  /***************** f1dim *************************/
    for(i1=1; i1<=ncodemax[k1];i1++){  extern int ncom; 
        j1++;  extern double *pcom,*xicom;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  extern double (*nrfunc)(double []); 
          scanf("%d", i);*/   
         for (i=-1; i<=nlstate+ndeath; i++)    double f1dim(double x) 
          for (jk=-1; jk<=nlstate+ndeath; jk++)    { 
            for(m=agemin; m <= agemax+3; m++)    int j; 
              freq[i][jk][m]=0;    double f;
     double *xt; 
         dateintsum=0;   
         k2cpt=0;    xt=vector(1,ncom); 
        for (i=1; i<=imx; i++) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
          bool=1;    f=(*nrfunc)(xt); 
          if  (cptcovn>0) {    free_vector(xt,1,ncom); 
            for (z1=1; z1<=cptcoveff; z1++)    return f; 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  } 
                bool=0;  
          }  /*****************brent *************************/
          if (bool==1) {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
            for(m=firstpass; m<=lastpass; m++){  { 
              k2=anint[m][i]+(mint[m][i]/12.);    int iter; 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    double a,b,d,etemp;
                if(agev[m][i]==0) agev[m][i]=agemax+1;    double fu=0,fv,fw,fx;
                if(agev[m][i]==1) agev[m][i]=agemax+2;    double ftemp=0.;
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double e=0.0; 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {   
                  dateintsum=dateintsum+k2;    a=(ax < cx ? ax : cx); 
                  k2cpt++;    b=(ax > cx ? ax : cx); 
                }    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
              }    for (iter=1;iter<=ITMAX;iter++) { 
            }      xm=0.5*(a+b); 
          }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
        }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
              printf(".");fflush(stdout);
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUGBRENT
         if  (cptcovn>0) {      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);
          fprintf(ficresp, "\n#********** Variable ");      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
        fprintf(ficresp, "**********\n#");  #endif
         }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
        for(i=1; i<=nlstate;i++)        *xmin=x; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        return fx; 
        fprintf(ficresp, "\n");      } 
              ftemp=fu;
   for(i=(int)agemin; i <= (int)agemax+3; i++){      if (fabs(e) > tol1) { 
     if(i==(int)agemax+3)        r=(x-w)*(fx-fv); 
       printf("Total");        q=(x-v)*(fx-fw); 
     else        p=(x-v)*q-(x-w)*r; 
       printf("Age %d", i);        q=2.0*(q-r); 
     for(jk=1; jk <=nlstate ; jk++){        if (q > 0.0) p = -p; 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        q=fabs(q); 
         pp[jk] += freq[jk][m][i];        etemp=e; 
     }        e=d; 
     for(jk=1; jk <=nlstate ; jk++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       for(m=-1, pos=0; m <=0 ; m++)          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         pos += freq[jk][m][i];        else { 
       if(pp[jk]>=1.e-10)          d=p/q; 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          u=x+d; 
       else          if (u-a < tol2 || b-u < tol2) 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            d=SIGN(tol1,xm-x); 
     }        } 
       } else { 
      for(jk=1; jk <=nlstate ; jk++){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      } 
         pp[jk] += freq[jk][m][i];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
      }      fu=(*f)(u); 
       if (fu <= fx) { 
     for(jk=1,pos=0; jk <=nlstate ; jk++)        if (u >= x) a=x; else b=x; 
       pos += pp[jk];        SHFT(v,w,x,u) 
     for(jk=1; jk <=nlstate ; jk++){          SHFT(fv,fw,fx,fu) 
       if(pos>=1.e-5)          } else { 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            if (u < x) a=u; else b=u; 
       else            if (fu <= fw || w == x) { 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              v=w; 
       if( i <= (int) agemax){              w=u; 
         if(pos>=1.e-5){              fv=fw; 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);              fw=fu; 
           probs[i][jk][j1]= pp[jk]/pos;            } else if (fu <= fv || v == x || v == w) { 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              v=u; 
         }              fv=fu; 
       else            } 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          } 
       }    } 
     }    nrerror("Too many iterations in brent"); 
     for(jk=-1; jk <=nlstate+ndeath; jk++)    *xmin=x; 
       for(m=-1; m <=nlstate+ndeath; m++)    return fx; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  } 
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  /****************** mnbrak ***********************/
     printf("\n");  
     }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     }              double (*func)(double)) 
  }  { 
   dateintmean=dateintsum/k2cpt;    double ulim,u,r,q, dum;
      double fu; 
   fclose(ficresp);   
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    *fa=(*func)(*ax); 
   free_vector(pp,1,nlstate);    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
   /* End of Freq */      SHFT(dum,*ax,*bx,dum) 
 }        SHFT(dum,*fb,*fa,dum) 
         } 
 /************ Prevalence ********************/    *cx=(*bx)+GOLD*(*bx-*ax); 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    *fc=(*func)(*cx); 
 {  /* Some frequencies */    while (*fb > *fc) { /* Declining fa, fb, fc */
        r=(*bx-*ax)*(*fb-*fc); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      q=(*bx-*cx)*(*fb-*fa); 
   double ***freq; /* Frequencies */      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double *pp;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
   double pos, k2;      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 */
   pp=vector(1,nlstate);        fu=(*func)(u); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  #ifdef DEBUG
          /* f(x)=A(x-u)**2+f(u) */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        double A, fparabu; 
   j1=0;        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
          fparabu= *fa - A*(*ax-u)*(*ax-u);
   j=cptcoveff;        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);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        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 
  for(k1=1; k1<=j;k1++){      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
     for(i1=1; i1<=ncodemax[k1];i1++){        fu=(*func)(u); 
       j1++;        if (fu < *fc) { 
            SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for (i=-1; i<=nlstate+ndeath; i++)              SHFT(*fb,*fc,fu,(*func)(u)) 
         for (jk=-1; jk<=nlstate+ndeath; jk++)              } 
           for(m=agemin; m <= agemax+3; m++)      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
             freq[i][jk][m]=0;        u=ulim; 
              fu=(*func)(u); 
       for (i=1; i<=imx; i++) {      } else { 
         bool=1;        u=(*cx)+GOLD*(*cx-*bx); 
         if  (cptcovn>0) {        fu=(*func)(u); 
           for (z1=1; z1<=cptcoveff; z1++)      } 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      SHFT(*ax,*bx,*cx,u) 
               bool=0;        SHFT(*fa,*fb,*fc,fu) 
         }        } 
         if (bool==1) {  } 
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  /*************** linmin ************************/
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
               if(agev[m][i]==0) agev[m][i]=agemax+1;  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
               if(agev[m][i]==1) agev[m][i]=agemax+2;  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  the value of func at the returned location p . This is actually all accomplished by calling the
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  routines mnbrak and brent .*/
             }  int ncom; 
           }  double *pcom,*xicom;
         }  double (*nrfunc)(double []); 
       }   
         for(i=(int)agemin; i <= (int)agemax+3; i++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           for(jk=1; jk <=nlstate ; jk++){  { 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double brent(double ax, double bx, double cx, 
               pp[jk] += freq[jk][m][i];                 double (*f)(double), double tol, double *xmin); 
           }    double f1dim(double x); 
           for(jk=1; jk <=nlstate ; jk++){    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
             for(m=-1, pos=0; m <=0 ; m++)                double *fc, double (*func)(double)); 
             pos += freq[jk][m][i];    int j; 
         }    double xx,xmin,bx,ax; 
            double fx,fb,fa;
          for(jk=1; jk <=nlstate ; jk++){   
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    ncom=n; 
              pp[jk] += freq[jk][m][i];    pcom=vector(1,n); 
          }    xicom=vector(1,n); 
              nrfunc=func; 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
          for(jk=1; jk <=nlstate ; jk++){                xicom[j]=xi[j]; 
            if( i <= (int) agemax){    } 
              if(pos>=1.e-5){    ax=0.0; 
                probs[i][jk][j1]= pp[jk]/pos;    xx=1.0; 
              }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
            }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
          }  #ifdef DEBUG
              printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
   }    for (j=1;j<=n;j++) { 
        xi[j] *= xmin; 
        p[j] += xi[j]; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    } 
   free_vector(pp,1,nlstate);    free_vector(xicom,1,n); 
      free_vector(pcom,1,n); 
 }  /* End of Freq */  } 
   
 /************* Waves Concatenation ***************/  
   /*************** powell ************************/
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  /*
 {  Minimization of a function func of n variables. Input consists of an initial starting point
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
      Death is a valid wave (if date is known).  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  such that failure to decrease by more than this amount on one iteration signals doneness. On
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
      and mw[mi+1][i]. dh depends on stepm.  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, 
   int i, mi, m;              double (*func)(double [])) 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  { 
      double sum=0., jmean=0.;*/    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   int j, k=0,jk, ju, jl;    int i,ibig,j; 
   double sum=0.;    double del,t,*pt,*ptt,*xit;
   jmin=1e+5;    double fp,fptt;
   jmax=-1;    double *xits;
   jmean=0.;    int niterf, itmp;
   for(i=1; i<=imx; i++){  
     mi=0;    pt=vector(1,n); 
     m=firstpass;    ptt=vector(1,n); 
     while(s[m][i] <= nlstate){    xit=vector(1,n); 
       if(s[m][i]>=1)    xits=vector(1,n); 
         mw[++mi][i]=m;    *fret=(*func)(p); 
       if(m >=lastpass)    for (j=1;j<=n;j++) pt[j]=p[j]; 
         break;      rcurr_time = time(NULL);  
       else    for (*iter=1;;++(*iter)) { 
         m++;      fp=(*fret); 
     }/* end while */      ibig=0; 
     if (s[m][i] > nlstate){      del=0.0; 
       mi++;     /* Death is another wave */      rlast_time=rcurr_time;
       /* if(mi==0)  never been interviewed correctly before death */      /* (void) gettimeofday(&curr_time,&tzp); */
          /* Only death is a correct wave */      rcurr_time = time(NULL);  
       mw[mi][i]=m;      curr_time = *localtime(&rcurr_time);
     }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
     wav[i]=mi;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
     if(mi==0)     for (i=1;i<=n;i++) {
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        printf(" %d %.12f",i, p[i]);
   }        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
   for(i=1; i<=imx; i++){      }
     for(mi=1; mi<wav[i];mi++){      printf("\n");
       if (stepm <=0)      fprintf(ficlog,"\n");
         dh[mi][i]=1;      fprintf(ficrespow,"\n");fflush(ficrespow);
       else{      if(*iter <=3){
         if (s[mw[mi+1][i]][i] > nlstate) {        tml = *localtime(&rcurr_time);
           if (agedc[i] < 2*AGESUP) {        strcpy(strcurr,asctime(&tml));
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        rforecast_time=rcurr_time; 
           if(j==0) j=1;  /* Survives at least one month after exam */        itmp = strlen(strcurr);
           k=k+1;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           if (j >= jmax) jmax=j;          strcurr[itmp-1]='\0';
           if (j <= jmin) jmin=j;        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           sum=sum+j;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for(niterf=10;niterf<=30;niterf+=10){
           }          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         }          forecast_time = *localtime(&rforecast_time);
         else{          strcpy(strfor,asctime(&forecast_time));
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          itmp = strlen(strfor);
           k=k+1;          if(strfor[itmp-1]=='\n')
           if (j >= jmax) jmax=j;          strfor[itmp-1]='\0';
           else if (j <= jmin)jmin=j;          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 (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          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);
           sum=sum+j;        }
         }      }
         jk= j/stepm;      for (i=1;i<=n;i++) { 
         jl= j -jk*stepm;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         ju= j -(jk+1)*stepm;        fptt=(*fret); 
         if(jl <= -ju)  #ifdef DEBUG
           dh[mi][i]=jk;            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
         else            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           dh[mi][i]=jk+1;  #endif
         if(dh[mi][i]==0)        printf("%d",i);fflush(stdout);
           dh[mi][i]=1; /* At least one step */        fprintf(ficlog,"%d",i);fflush(ficlog);
       }        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
   jmean=sum/k;          ibig=i; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        } 
  }  #ifdef DEBUG
 /*********** Tricode ****************************/        printf("%d %.12e",i,(*fret));
 void tricode(int *Tvar, int **nbcode, int imx)        fprintf(ficlog,"%d %.12e",i,(*fret));
 {        for (j=1;j<=n;j++) {
   int Ndum[20],ij=1, k, j, i;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   int cptcode=0;          printf(" x(%d)=%.12e",j,xit[j]);
   cptcoveff=0;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
          }
   for (k=0; k<19; k++) Ndum[k]=0;        for(j=1;j<=n;j++) {
   for (k=1; k<=7; k++) ncodemax[k]=0;          printf(" p(%d)=%.12e",j,p[j]);
           fprintf(ficlog," p(%d)=%.12e",j,p[j]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        }
     for (i=1; i<=imx; i++) {        printf("\n");
       ij=(int)(covar[Tvar[j]][i]);        fprintf(ficlog,"\n");
       Ndum[ij]++;  #endif
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      } /* end i */
       if (ij > cptcode) cptcode=ij;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
         int k[2],l;
     for (i=0; i<=cptcode; i++) {        k[0]=1;
       if(Ndum[i]!=0) ncodemax[j]++;        k[1]=-1;
     }        printf("Max: %.12e",(*func)(p));
     ij=1;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
     for (i=1; i<=ncodemax[j]; i++) {          fprintf(ficlog," %.12e",p[j]);
       for (k=0; k<=19; k++) {        }
         if (Ndum[k] != 0) {        printf("\n");
           nbcode[Tvar[j]][ij]=k;        fprintf(ficlog,"\n");
           ij++;        for(l=0;l<=1;l++) {
         }          for (j=1;j<=n;j++) {
         if (ij > ncodemax[j]) break;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       }              printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   }            }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
  for (k=0; k<19; k++) Ndum[k]=0;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
  for (i=1; i<=ncovmodel-2; i++) {  #endif
       ij=Tvar[i];  
       Ndum[ij]++;  
     }        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
  ij=1;        free_vector(ptt,1,n); 
  for (i=1; i<=10; i++) {        free_vector(pt,1,n); 
    if((Ndum[i]!=0) && (i<=ncov)){        return; 
      Tvaraff[ij]=i;      } 
      ij++;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
    }      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
  }        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
     cptcoveff=ij-1;        pt[j]=p[j]; 
 }      } 
       fptt=(*func)(ptt); 
 /*********** Health Expectancies ****************/      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
         /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
 {        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
   /* Health expectancies */        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   int i, j, nhstepm, hstepm, h, nstepm, k;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
   double age, agelim,hf;        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
   double ***p3mat;        /* Thus we compare delta(2h) with observed f1-f3 */
          /* or best gain on one ancient line 'del' with total  */
   fprintf(ficreseij,"# Health expectancies\n");        /* gain f1-f2 = f1 - f2 - 'del' with del  */
   fprintf(ficreseij,"# Age");        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
       fprintf(ficreseij," %1d-%1d",i,j);        t= t- del*SQR(fp-fptt);
   fprintf(ficreseij,"\n");        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);
   k=1;             /* For example stepm=6 months */  #ifdef DEBUG
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
      nhstepm is the number of hstepm from age to agelim               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
      nstepm is the number of stepm from age to agelin.        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);
      Look at hpijx to understand the reason of that which relies in memory size        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);
      and note for a fixed period like k years */  #endif
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        if (t < 0.0) { /* Then we use it for last direction */
      survival function given by stepm (the optimization length). Unfortunately it          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
      means that if the survival funtion is printed only each two years of age and if          for (j=1;j<=n;j++) { 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
      results. So we changed our mind and took the option of the best precision.            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   */          }
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
           fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #ifdef DEBUG
     /* nhstepm age range expressed in number of stepm */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          for(j=1;j<=n;j++){
     /* if (stepm >= YEARM) hstepm=1;*/            printf(" %.12e",xit[j]);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            fprintf(ficlog," %.12e",xit[j]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          printf("\n");
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          fprintf(ficlog,"\n");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    #endif
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        } /* end of t negative */
     for(i=1; i<=nlstate;i++)      } /* end if (fptt < fp)  */
       for(j=1; j<=nlstate;j++)    } 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  } 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[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]);*/  /**** Prevalence limit (stable or period prevalence)  ****************/
         }  
     fprintf(ficreseij,"%3.0f",age );  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
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);       matrix by transitions matrix until convergence is reached */
       }    
     fprintf(ficreseij,"\n");    int i, ii,j,k;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double min, max, maxmin, maxmax,sumnew=0.;
   }    /* double **matprod2(); */ /* test */
 }    double **out, cov[NCOVMAX+1], **pmij();
     double **newm;
 /************ Variance ******************/    double agefin, delaymax=50 ; /* Max number of years to converge */
 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 (ii=1;ii<=nlstate+ndeath;ii++)
   /* Variance of health expectancies */      for (j=1;j<=nlstate+ndeath;j++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **newm;      }
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm, h;    cov[1]=1.;
   int k, cptcode;    
   double *xp;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double **gp, **gm;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double ***gradg, ***trgradg;      newm=savm;
   double ***p3mat;      /* Covariates have to be included here again */
   double age,agelim;      cov[2]=agefin;
   int theta;      
       for (k=1; k<=cptcovn;k++) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   fprintf(ficresvij,"# Age");        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   fprintf(ficresvij,"\n");      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
       
   xp=vector(1,npar);      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   dnewm=matrix(1,nlstate,1,npar);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   doldm=matrix(1,nlstate,1,nlstate);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
        /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   hstepm=1*YEARM; /* Every year of age */      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   agelim = AGESUP;      
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      savm=oldm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      oldm=newm;
     if (stepm >= YEARM) hstepm=1;      maxmax=0.;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for(j=1;j<=nlstate;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        min=1.;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        max=0.;
     gp=matrix(0,nhstepm,1,nlstate);        for(i=1; i<=nlstate; i++) {
     gm=matrix(0,nhstepm,1,nlstate);          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for(theta=1; theta <=npar; theta++){          prlim[i][j]= newm[i][j]/(1-sumnew);
       for(i=1; i<=npar; i++){ /* Computes gradient */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          max=FMAX(max,prlim[i][j]);
       }          min=FMIN(min,prlim[i][j]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
       if (popbased==1) {      } /* j loop */
         for(i=1; i<=nlstate;i++)      if(maxmax < ftolpl){
           prlim[i][i]=probs[(int)age][i][ij];        return prlim;
       }      }
      } /* age loop */
       for(j=1; j<= nlstate; j++){    return prlim; /* should not reach here */
         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];  /*************** transition probabilities ***************/ 
         }  
       }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      {
       for(i=1; i<=npar; i++) /* Computes gradient */    /* According to parameters values stored in x and the covariate's values stored in cov,
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       computes the probability to be observed in state j being in state i by appying the
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         model to the ncovmodel covariates (including constant and age).
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         and, according on how parameters are entered, the position of the coefficient xij(nc) of the
       if (popbased==1) {       ncth covariate in the global vector x is given by the formula:
         for(i=1; i<=nlstate;i++)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           prlim[i][i]=probs[(int)age][i][ij];       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       }       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       for(j=1; j<= nlstate; j++){       Outputs ps[i][j] the probability to be observed in j being in j according to
         for(h=0; h<=nhstepm; h++){       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double s1, lnpijopii;
         }    /*double t34;*/
       }    int i,j, nc, ii, jj;
   
       for(j=1; j<= nlstate; j++)      for(i=1; i<= nlstate; i++){
         for(h=0; h<=nhstepm; h++){        for(j=1; j<i;j++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         }            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     } /* End theta */            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",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++)  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       for(j=1; j<=nlstate;j++)        }
         for(theta=1; theta <=npar; theta++)        for(j=i+1; j<=nlstate+ndeath;j++){
           trgradg[h][j][theta]=gradg[h][theta][j];          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     for(i=1;i<=nlstate;i++)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       for(j=1;j<=nlstate;j++)  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         vareij[i][j][(int)age] =0.;          }
     for(h=0;h<=nhstepm;h++){          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       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(i=1; i<= nlstate; i++){
           for(j=1;j<=nlstate;j++)        s1=0;
             vareij[i][j][(int)age] += doldm[i][j];        for(j=1; j<i; j++){
       }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     }          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     h=1;        }
     if (stepm >= YEARM) h=stepm/YEARM;        for(j=i+1; j<=nlstate+ndeath; j++){
     fprintf(ficresvij,"%.0f ",age );          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     for(i=1; i<=nlstate;i++)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       for(j=1; j<=nlstate;j++){        }
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       }        ps[i][i]=1./(s1+1.);
     fprintf(ficresvij,"\n");        /* Computing other pijs */
     free_matrix(gp,0,nhstepm,1,nlstate);        for(j=1; j<i; j++)
     free_matrix(gm,0,nhstepm,1,nlstate);          ps[i][j]= exp(ps[i][j])*ps[i][i];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for(j=i+1; j<=nlstate+ndeath; j++)
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   } /* End age */      } /* end i */
        
   free_vector(xp,1,npar);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   free_matrix(doldm,1,nlstate,1,npar);        for(jj=1; jj<= nlstate+ndeath; jj++){
   free_matrix(dnewm,1,nlstate,1,nlstate);          ps[ii][jj]=0;
           ps[ii][ii]=1;
 }        }
       }
 /************ 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(ii=1; ii<= nlstate+ndeath; ii++){ */
   /* Variance of prevalence limit */      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   double **newm;      /*   } */
   double **dnewm,**doldm;      /*   printf("\n "); */
   int i, j, nhstepm, hstepm;      /* } */
   int k, cptcode;      /* printf("\n ");printf("%lf ",cov[2]);*/
   double *xp;      /*
   double *gp, *gm;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double **gradg, **trgradg;        goto end;*/
   double age,agelim;      return ps;
   int theta;  }
      
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  /**************** Product of 2 matrices ******************/
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       fprintf(ficresvpl," %1d-%1d",i,i);  {
   fprintf(ficresvpl,"\n");    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   xp=vector(1,npar);    /* in, b, out are matrice of pointers which should have been initialized 
   dnewm=matrix(1,nlstate,1,npar);       before: only the contents of out is modified. The function returns
   doldm=matrix(1,nlstate,1,nlstate);       a pointer to pointers identical to out */
      int i, j, k;
   hstepm=1*YEARM; /* Every year of age */    for(i=nrl; i<= nrh; i++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for(k=ncolol; k<=ncoloh; k++){
   agelim = AGESUP;        out[i][k]=0.;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for(j=ncl; j<=nch; j++)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          out[i][k] +=in[i][j]*b[j][k];
     if (stepm >= YEARM) hstepm=1;      }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    return out;
     gradg=matrix(1,npar,1,nlstate);  }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);  
   /************* Higher Matrix Product ***************/
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    /* Computes the transition matrix starting at age 'age' over 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       'nhstepm*hstepm*stepm' months (i.e. until
       for(i=1;i<=nlstate;i++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         gp[i] = prlim[i][i];       nhstepm*hstepm matrices. 
           Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       for(i=1; i<=npar; i++) /* Computes gradient */       (typically every 2 years instead of every month which is too big 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       for the memory).
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       Model is determined by parameters x and covariates have to be 
       for(i=1;i<=nlstate;i++)       included manually here. 
         gm[i] = prlim[i][i];  
        */
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int i, j, d, h, k;
     } /* End theta */    double **out, cov[NCOVMAX+1];
     double **newm;
     trgradg =matrix(1,nlstate,1,npar);  
     /* Hstepm could be zero and should return the unit matrix */
     for(j=1; j<=nlstate;j++)    for (i=1;i<=nlstate+ndeath;i++)
       for(theta=1; theta <=npar; theta++)      for (j=1;j<=nlstate+ndeath;j++){
         trgradg[j][theta]=gradg[theta][j];        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
     for(i=1;i<=nlstate;i++)      }
       varpl[i][(int)age] =0.;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    for(h=1; h <=nhstepm; h++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      for(d=1; d <=hstepm; d++){
     for(i=1;i<=nlstate;i++)        newm=savm;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        /* Covariates have to be included here again */
         cov[1]=1.;
     fprintf(ficresvpl,"%.0f ",age );        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     fprintf(ficresvpl,"\n");        for (k=1; k<=cptcovage;k++)
     free_vector(gp,1,nlstate);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     free_vector(gm,1,nlstate);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
     free_matrix(gradg,1,npar,1,nlstate);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   free_vector(xp,1,npar);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   free_matrix(doldm,1,nlstate,1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   free_matrix(dnewm,1,nlstate,1,nlstate);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
 }        oldm=newm;
       }
 /************ Variance of one-step probabilities  ******************/      for(i=1; i<=nlstate+ndeath; i++)
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        for(j=1;j<=nlstate+ndeath;j++) {
 {          po[i][j][h]=newm[i][j];
   int i, j;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   int k=0, cptcode;        }
   double **dnewm,**doldm;      /*printf("h=%d ",h);*/
   double *xp;    } /* end h */
   double *gp, *gm;  /*     printf("\n H=%d \n",h); */
   double **gradg, **trgradg;    return po;
   double age,agelim, cov[NCOVMAX];  }
   int theta;  
   char fileresprob[FILENAMELENGTH];  #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   strcpy(fileresprob,"prob");    double fret;
   strcat(fileresprob,fileres);    double *xt;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    int j;
     printf("Problem with resultfile: %s\n", fileresprob);    myfunc_data *d2 = (myfunc_data *) pd;
   }  /* xt = (p1-1); */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    xt=vector(1,n); 
      for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   
   xp=vector(1,npar);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    printf("Function = %.12lf ",fret);
      for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
   cov[1]=1;    printf("\n");
   for (age=bage; age<=fage; age ++){   free_vector(xt,1,n);
     cov[2]=age;    return fret;
     gradg=matrix(1,npar,1,9);  }
     trgradg=matrix(1,9,1,npar);  #endif
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  /*************** log-likelihood *************/
      double func( double *x)
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++)    int i, ii, j, k, mi, d, kk;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
          double **out;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double sw; /* Sum of weights */
        double lli; /* Individual log likelihood */
       k=0;    int s1, s2;
       for(i=1; i<= (nlstate+ndeath); i++){    double bbh, survp;
         for(j=1; j<=(nlstate+ndeath);j++){    long ipmx;
            k=k+1;    /*extern weight */
           gp[k]=pmmij[i][j];    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
       for(i=1; i<=npar; i++)    */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
        ++countcallfunc;
   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    cov[1]=1.;
       k=0;  
       for(i=1; i<=(nlstate+ndeath); i++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(j=1; j<=(nlstate+ndeath);j++){  
           k=k+1;    if(mle==1){
           gm[k]=pmmij[i][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        /* 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
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)           to be observed in j being in i according to the model.
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];           */
     }        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
           cov[2+k]=covar[Tvar[k]][i];
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        }
       for(theta=1; theta <=npar; theta++)        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       trgradg[j][theta]=gradg[theta][j];           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
             has been calculated etc */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        for(mi=1; mi<= wav[i]-1; mi++){
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
      pmij(pmmij,cov,ncovmodel,x,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
      k=0;            }
      for(i=1; i<=(nlstate+ndeath); i++){          for(d=0; d<dh[mi][i]; d++){
        for(j=1; j<=(nlstate+ndeath);j++){            newm=savm;
          k=k+1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          gm[k]=pmmij[i][j];            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
      }            }
                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      /*printf("\n%d ",(int)age);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            savm=oldm;
                    oldm=newm;
           } /* end mult */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        
      }*/          /*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.
   fprintf(ficresprob,"\n%d ",(int)age);           * 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 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);           * (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
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));           * -stepm/2 to stepm/2 .
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));           * For stepm=1 the results are the same as for previous versions of Imach.
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);           * For stepm > 1 the results are less biased than in previous versions. 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);           */
 }          s1=s[mw[mi][i]][i];
  free_vector(xp,1,npar);          s2=s[mw[mi+1][i]][i];
 fclose(ficresprob);          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
 }           * is higher than the multiple of stepm and negative otherwise.
            */
 /******************* Printing html file ***********/          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){          if( s2 > nlstate){ 
   int jj1, k1, i1, cpt;            /* i.e. if s2 is a death state and if the date of death is known 
   FILE *fichtm;               then the contribution to the likelihood is the probability to 
   /*char optionfilehtm[FILENAMELENGTH];*/               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
   strcpy(optionfilehtm,optionfile);               minus probability to die before dh-stepm . 
   strcat(optionfilehtm,".htm");               In version up to 0.92 likelihood was computed
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          as if date of death was unknown. Death was treated as any other
     printf("Problem with %s \n",optionfilehtm), exit(0);          health state: the date of the interview describes the actual state
   }          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71e </font> <hr size=\"2\" color=\"#EC5E5E\">          (healthy, disable or death) and IMaCh was corrected; but when we
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
 Total number of observations=%d <br>          contribution is smaller and very dependent of the step unit
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          stepm. It is no more the probability to die between last interview
 <hr  size=\"2\" color=\"#EC5E5E\">          and month of death but the probability to survive from last
 <li>Outputs files<br><br>\n          interview up to one month before death multiplied by the
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          probability to die within a month. Thanks to Chris
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          Jackson for correcting this bug.  Former versions increased
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          mortality artificially. The bad side is that we add another loop
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>          which slows down the processing. The difference can be up to 10%
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          lower mortality.
         - 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>            lli=log(out[s1][s2] - savm[s1][s2]);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>          } else if  (s2==-2) {
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>            for (j=1,survp=0. ; j<=nlstate; j++) 
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
              /*survp += out[s1][j]; */
 fprintf(fichtm," <li>Graphs</li><p>");            lli= log(survp);
           }
  m=cptcoveff;          
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
  jj1=0;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
  for(k1=1; k1<=m;k1++){            lli= log(survp); 
    for(i1=1; i1<=ncodemax[k1];i1++){          } 
        jj1++;  
        if (cptcovn > 0) {          else if  (s2==-5) { 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            for (j=1,survp=0. ; j<=2; j++)  
          for (cpt=1; cpt<=cptcoveff;cpt++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            lli= log(survp); 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          } 
        }          
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          else{
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        for(cpt=1; cpt<nlstate;cpt++){            /*  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,"<br>- Prevalence of disability : p%s%d%d.gif<br>          } 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
        }          /*if(lli ==000.0)*/
     for(cpt=1; cpt<=nlstate;cpt++) {          /*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); */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          ipmx +=1;
 interval) in state (%d): v%s%d%d.gif <br>          sw += weight[i];
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      }        } /* end of wave */
      for(cpt=1; cpt<=nlstate;cpt++) {      } /* end of individual */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    }  else if(mle==2){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for(mi=1; mi<= wav[i]-1; mi++){
 health expectancies in states (1) and (2): e%s%d.gif<br>          for (ii=1;ii<=nlstate+ndeath;ii++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            for (j=1;j<=nlstate+ndeath;j++){
 fprintf(fichtm,"\n</body>");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    }            }
 fclose(fichtm);          for(d=0; d<=dh[mi][i]; d++){
 }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /******************* Gnuplot file **************/            for (kk=1; kk<=cptcovage;kk++) {
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   strcpy(optionfilegnuplot,optionfilefiname);            savm=oldm;
   strcat(optionfilegnuplot,".plt");            oldm=newm;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          } /* end mult */
     printf("Problem with file %s",optionfilegnuplot);        
   }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 #ifdef windows          bbh=(double)bh[mi][i]/(double)stepm; 
     fprintf(ficgp,"cd \"%s\" \n",pathc);          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 */
 #endif          ipmx +=1;
 m=pow(2,cptcoveff);          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  /* 1eme*/        } /* end of wave */
   for (cpt=1; cpt<= nlstate ; cpt ++) {      } /* end of individual */
    for (k1=1; k1<= m ; k1 ++) {    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 #ifdef windows        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);        for(mi=1; mi<= wav[i]-1; mi++){
 #endif          for (ii=1;ii<=nlstate+ndeath;ii++)
 #ifdef unix            for (j=1;j<=nlstate+ndeath;j++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #endif              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 for (i=1; i<= nlstate ; i ++) {          for(d=0; d<dh[mi][i]; d++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            newm=savm;
   else fprintf(ficgp," \%%*lf (\%%*lf)");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (i=1; i<= nlstate ; i ++) {            }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   else fprintf(ficgp," \%%*lf (\%%*lf)");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            oldm=newm;
      for (i=1; i<= nlstate ; i ++) {          } /* end mult */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        
   else fprintf(ficgp," \%%*lf (\%%*lf)");          s1=s[mw[mi][i]][i];
 }            s2=s[mw[mi+1][i]][i];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          bbh=(double)bh[mi][i]/(double)stepm; 
 #ifdef unix          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 fprintf(ficgp,"\nset ter gif small size 400,300");          ipmx +=1;
 #endif          sw += weight[i];
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    }        } /* end of wave */
   }      } /* end of individual */
   /*2 eme*/    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (k1=1; k1<= m ; k1 ++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        for(mi=1; mi<= wav[i]-1; mi++){
              for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=1; i<= nlstate+1 ; i ++) {            for (j=1;j<=nlstate+ndeath;j++){
       k=2*i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (j=1; j<= nlstate+1 ; j ++) {            }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(d=0; d<dh[mi][i]; d++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            newm=savm;
 }              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            for (kk=1; kk<=cptcovage;kk++) {
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            }
       for (j=1; j<= nlstate+1 ; j ++) {          
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         else fprintf(ficgp," \%%*lf (\%%*lf)");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }              savm=oldm;
       fprintf(ficgp,"\" t\"\" w l 0,");            oldm=newm;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          } /* end mult */
       for (j=1; j<= nlstate+1 ; j ++) {        
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          s1=s[mw[mi][i]][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          s2=s[mw[mi+1][i]][i];
 }            if( s2 > nlstate){ 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            lli=log(out[s1][s2] - savm[s1][s2]);
       else fprintf(ficgp,"\" t\"\" w l 0,");          }else{
     }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          }
   }          ipmx +=1;
            sw += weight[i];
   /*3eme*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   for (k1=1; k1<= m ; k1 ++) {        } /* end of wave */
     for (cpt=1; cpt<= nlstate ; cpt ++) {      } /* end of individual */
       k=2+nlstate*(cpt-1);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (i=1; i< nlstate ; i ++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         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);        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficgp,"\nset out \"exp%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);
              }
   /* CV preval stat */          for(d=0; d<dh[mi][i]; d++){
     for (k1=1; k1<= m ; k1 ++) {            newm=savm;
     for (cpt=1; cpt<nlstate ; cpt ++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       k=3;            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
       for (i=1; i< nlstate ; i ++)          
         fprintf(ficgp,"+$%d",k+i+1);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  savm=oldm;
       l=3+(nlstate+ndeath)*cpt;            oldm=newm;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          } /* end mult */
       for (i=1; i< nlstate ; i ++) {        
         l=3+(nlstate+ndeath)*cpt;          s1=s[mw[mi][i]][i];
         fprintf(ficgp,"+$%d",l+i+1);          s2=s[mw[mi+1][i]][i];
       }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            ipmx +=1;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }            /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
          } /* end of wave */
   /* proba elementaires */      } /* end of individual */
    for(i=1,jk=1; i <=nlstate; i++){    } /* End of if */
     for(k=1; k <=(nlstate+ndeath); k++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       if (k != i) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         for(j=1; j <=ncovmodel; j++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
            return -l;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  }
           jk++;  
           fprintf(ficgp,"\n");  /*************** log-likelihood *************/
         }  double funcone( double *x)
       }  {
     }    /* Same as likeli but slower because of a lot of printf and if */
     }    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     for(jk=1; jk <=m; jk++) {    double **out;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    double lli; /* Individual log likelihood */
    i=1;    double llt;
    for(k2=1; k2<=nlstate; k2++) {    int s1, s2;
      k3=i;    double bbh, survp;
      for(k=1; k<=(nlstate+ndeath); k++) {    /*extern weight */
        if (k != k2){    /* We are differentiating ll according to initial status */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 ij=1;    /*for(i=1;i<imx;i++) 
         for(j=3; j <=ncovmodel; j++) {      printf(" %d\n",s[4][i]);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    cov[1]=1.;
             ij++;  
           }    for(k=1; k<=nlstate; k++) ll[k]=0.;
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           fprintf(ficgp,")/(1");      for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
         for(k1=1; k1 <=nlstate; k1++){            for (j=1;j<=nlstate+ndeath;j++){
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 ij=1;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(j=3; j <=ncovmodel; j++){          }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for(d=0; d<dh[mi][i]; d++){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          newm=savm;
             ij++;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }          for (kk=1; kk<=cptcovage;kk++) {
           else            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
           }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           fprintf(ficgp,")");          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
         i=i+ncovmodel;          savm=oldm;
        }          oldm=newm;
      }        } /* end mult */
    }        
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        s1=s[mw[mi][i]][i];
    }        s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   fclose(ficgp);        /* bias is positive if real duration
 }  /* end gnuplot */         * is higher than the multiple of stepm and negative otherwise.
          */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
 /*************** Moving average **************/          lli=log(out[s1][s2] - savm[s1][s2]);
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
   int i, cpt, cptcod;            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for (agedeb=agemin; agedeb<=fage; agedeb++)          lli= log(survp);
       for (i=1; i<=nlstate;i++)        }else if (mle==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.;        } else if(mle==2){
              lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){        } else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1; i<=nlstate;i++){          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 */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           for (cpt=0;cpt<=4;cpt++){          lli=log(out[s1][s2]); /* Original formula */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        } else{  /* mle=0 back to 1 */
           }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          /*lli=log(out[s1][s2]); */ /* Original formula */
         }        } /* End of if */
       }        ipmx +=1;
     }        sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 }        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
           fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
 /************** Forecasting ******************/   %11.6f %11.6f %11.6f ", \
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){                  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]);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   int *popage;            llt +=ll[k]*gipmx/gsw;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double *popeffectif,*popcount;          }
   double ***p3mat;          fprintf(ficresilk," %10.6f\n", -llt);
   char fileresf[FILENAMELENGTH];        }
       } /* end of wave */
  agelim=AGESUP;    } /* end of individual */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      if(globpr==0){ /* First time we count the contributions and weights */
        gipmx=ipmx;
   strcpy(fileresf,"f");      gsw=sw;
   strcat(fileresf,fileres);    }
   if((ficresf=fopen(fileresf,"w"))==NULL) {    return -l;
     printf("Problem with forecast resultfile: %s\n", fileresf);  }
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   /*************** function likelione ***********/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
   if (mobilav==1) {    /* This routine should help understanding what is done with 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       the selection of individuals/waves and
     movingaverage(agedeb, fage, agemin, mobaverage);       to check the exact contribution to the likelihood.
   }       Plotting could be done.
      */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int k;
   if (stepm<=12) stepsize=1;  
      if(*globpri !=0){ /* Just counts and sums, no printings */
   agelim=AGESUP;      strcpy(fileresilk,"ilk"); 
        strcat(fileresilk,fileres);
   hstepm=1;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   hstepm=hstepm/stepm;        printf("Problem with resultfile: %s\n", fileresilk);
   yp1=modf(dateintmean,&yp);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   anprojmean=yp;      }
   yp2=modf((yp1*12),&yp);      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");
   mprojmean=yp;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   yp1=modf((yp2*30.5),&yp);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   jprojmean=yp;      for(k=1; k<=nlstate; k++) 
   if(jprojmean==0) jprojmean=1;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   if(mprojmean==0) jprojmean=1;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
      *fretone=(*funcone)(p);
   for(cptcov=1;cptcov<=i2;cptcov++){    if(*globpri !=0){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fclose(ficresilk);
       k=k+1;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fprintf(ficresf,"\n#******");      fflush(fichtm); 
       for(j=1;j<=cptcoveff;j++) {    } 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    return;
       }  }
       fprintf(ficresf,"******\n");  
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  /*********** Maximum Likelihood Estimation ***************/
        
        void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  {
         fprintf(ficresf,"\n");    int i,j, iter=0;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      double **xi;
     double fret;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    double fretone; /* Only one call to likelihood */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /*  char filerespow[FILENAMELENGTH];*/
           nhstepm = nhstepm/hstepm;  
            #ifdef NLOPT
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int creturn;
           oldm=oldms;savm=savms;    nlopt_opt opt;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /* 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;
           for (h=0; h<=nhstepm; h++){    double minf; /* the minimum objective value, upon return */
             if (h==(int) (calagedate+YEARM*cpt)) {    double * p1; /* Shifted parameters from 0 instead of 1 */
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    myfunc_data dinst, *d = &dinst;
             }  #endif
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  xi=matrix(1,npar,1,npar);
                 if (mobilav==1)    for (i=1;i<=npar;i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for (j=1;j<=npar;j++)
                 else {        xi[i][j]=(i==j ? 1.0 : 0.0);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
                 }    strcpy(filerespow,"pow"); 
                    strcat(filerespow,fileres);
               }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
               if (h==(int)(calagedate+12*cpt)){      printf("Problem with resultfile: %s\n", filerespow);
                 fprintf(ficresf," %.3f", kk1);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                            }
               }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
             }    for (i=1;i<=nlstate;i++)
           }      for(j=1;j<=nlstate+ndeath;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         }    fprintf(ficrespow,"\n");
       }  #ifdef POWELL
     }    powell(p,xi,npar,ftol,&iter,&fret,func);
   }  #endif
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  #ifdef NLOPT
   #ifdef NEWUOA
   fclose(ficresf);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
 }  #else
 /************** Forecasting ******************/    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  #endif
      lb=vector(0,npar-1);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   int *popage;    nlopt_set_lower_bounds(opt, lb);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    nlopt_set_initial_step1(opt, 0.1);
   double *popeffectif,*popcount;    
   double ***p3mat,***tabpop,***tabpopprev;    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   char filerespop[FILENAMELENGTH];    d->function = func;
     printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    nlopt_set_min_objective(opt, myfunc, d);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    nlopt_set_xtol_rel(opt, ftol);
   agelim=AGESUP;    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      printf("nlopt failed! %d\n",creturn); 
      }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    else {
        printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
        printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
   strcpy(filerespop,"pop");      iter=1; /* not equal */
   strcat(filerespop,fileres);    }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    nlopt_destroy(opt);
     printf("Problem with forecast resultfile: %s\n", filerespop);  #endif
   }    free_matrix(xi,1,npar,1,npar);
   printf("Computing forecasting: result on file '%s' \n", filerespop);    fclose(ficrespow);
     printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
     movingaverage(agedeb, fage, agemin, mobaverage);  
   }  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   stepsize=(int) (stepm+YEARM-1)/YEARM;  {
   if (stepm<=12) stepsize=1;    double  **a,**y,*x,pd;
      double **hess;
   agelim=AGESUP;    int i, j;
      int *indx;
   hstepm=1;  
   hstepm=hstepm/stepm;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
      double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   if (popforecast==1) {    void lubksb(double **a, int npar, int *indx, double b[]) ;
     if((ficpop=fopen(popfile,"r"))==NULL) {    void ludcmp(double **a, int npar, int *indx, double *d) ;
       printf("Problem with population file : %s\n",popfile);exit(0);    double gompertz(double p[]);
     }    hess=matrix(1,npar,1,npar);
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);    printf("\nCalculation of the hessian matrix. Wait...\n");
     popcount=vector(0,AGESUP);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
        for (i=1;i<=npar;i++){
     i=1;        printf("%d",i);fflush(stdout);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      fprintf(ficlog,"%d",i);fflush(ficlog);
         
     imx=i;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      
   }      /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   for(cptcov=1;cptcov<=i2;cptcov++){    }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
       k=k+1;    for (i=1;i<=npar;i++) {
       fprintf(ficrespop,"\n#******");      for (j=1;j<=npar;j++)  {
       for(j=1;j<=cptcoveff;j++) {        if (j>i) { 
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          printf(".%d%d",i,j);fflush(stdout);
       }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       fprintf(ficrespop,"******\n");          hess[i][j]=hessij(p,delti,i,j,func,npar);
       fprintf(ficrespop,"# Age");          
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          hess[j][i]=hess[i][j];    
       if (popforecast==1)  fprintf(ficrespop," [Population]");          /*printf(" %lf ",hess[i][j]);*/
              }
       for (cpt=0; cpt<=0;cpt++) {      }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      }
            printf("\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    fprintf(ficlog,"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
              fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;    a=matrix(1,npar,1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      y=matrix(1,npar,1,npar);
            x=vector(1,npar);
           for (h=0; h<=nhstepm; h++){    indx=ivector(1,npar);
             if (h==(int) (calagedate+YEARM*cpt)) {    for (i=1;i<=npar;i++)
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
             }    ludcmp(a,npar,indx,&pd);
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    for (j=1;j<=npar;j++) {
               for(i=1; i<=nlstate;i++) {                    for (i=1;i<=npar;i++) x[i]=0;
                 if (mobilav==1)      x[j]=1;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      lubksb(a,npar,indx,x);
                 else {      for (i=1;i<=npar;i++){ 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        matcov[i][j]=x[i];
                 }      }
               }    }
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    printf("\n#Hessian matrix#\n");
                   /*fprintf(ficrespop," %.3f", kk1);    fprintf(ficlog,"\n#Hessian matrix#\n");
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    for (i=1;i<=npar;i++) { 
               }      for (j=1;j<=npar;j++) { 
             }        printf("%.3e ",hess[i][j]);
             for(i=1; i<=nlstate;i++){        fprintf(ficlog,"%.3e ",hess[i][j]);
               kk1=0.;      }
                 for(j=1; j<=nlstate;j++){      printf("\n");
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      fprintf(ficlog,"\n");
                 }    }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  
             }    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    ludcmp(a,npar,indx,&pd);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*  printf("\n#Hessian matrix recomputed#\n");
         }  
       }    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   /******/      x[j]=1;
       lubksb(a,npar,indx,x);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      for (i=1;i<=npar;i++){ 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          y[i][j]=x[i];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        printf("%.3e ",y[i][j]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficlog,"%.3e ",y[i][j]);
           nhstepm = nhstepm/hstepm;      }
                printf("\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"\n");
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    free_matrix(a,1,npar,1,npar);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    free_matrix(y,1,npar,1,npar);
             }    free_vector(x,1,npar);
             for(j=1; j<=nlstate+ndeath;j++) {    free_ivector(indx,1,npar);
               kk1=0.;kk2=0;    free_matrix(hess,1,npar,1,npar);
               for(i=1; i<=nlstate;i++) {                
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }  }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }  /*************** hessian matrix ****************/
           }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
         }    int i;
       }    int l=1, lmax=20;
    }    double k1,k2;
   }    double p2[MAXPARM+1]; /* identical to x */
      double res;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
   if (popforecast==1) {    int k=0,kmax=10;
     free_ivector(popage,0,AGESUP);    double l1;
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);    fx=func(x);
   }    for (i=1;i<=npar;i++) p2[i]=x[i];
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      l1=pow(10,l);
   fclose(ficrespop);      delts=delt;
 }      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
 /***********************************************/        p2[theta]=x[theta] +delt;
 /**************** Main Program *****************/        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
 /***********************************************/        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
 int main(int argc, char *argv[])        /*res= (k1-2.0*fx+k2)/delt/delt; */
 {        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  #ifdef DEBUGHESS
   double agedeb, agefin,hf;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
   double fret;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   double **xi,tmp,delta;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
   double dum; /* Dummy variable */        }
   double ***p3mat;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   int *indx;          k=kmax; l=lmax*10;
   char line[MAXLINE], linepar[MAXLINE];        }
   char title[MAXLINE];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          delts=delt;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        }
        }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    }
     delti[theta]=delts;
   char filerest[FILENAMELENGTH];    return res; 
   char fileregp[FILENAMELENGTH];    
   char popfile[FILENAMELENGTH];  }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   int sdeb, sfin; /* Status at beginning and end */  {
   int c,  h , cpt,l;    int i;
   int ju,jl, mi;    int l=1, lmax=20;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    double k1,k2,k3,k4,res,fx;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    double p2[MAXPARM+1];
   int mobilav=0,popforecast=0;    int k;
   int hstepm, nhstepm;  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    fx=func(x);
     for (k=1; k<=2; k++) {
   double bage, fage, age, agelim, agebase;      for (i=1;i<=npar;i++) p2[i]=x[i];
   double ftolpl=FTOL;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double **prlim;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double *severity;      k1=func(p2)-fx;
   double ***param; /* Matrix of parameters */    
   double  *p;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double **matcov; /* Matrix of covariance */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double ***delti3; /* Scale */      k2=func(p2)-fx;
   double *delti; /* Scale */    
   double ***eij, ***vareij;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double **varpl; /* Variances of prevalence limits by age */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double *epj, vepp;      k3=func(p2)-fx;
   double kk1, kk2;    
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
   char version[80]="Imach version 0.71e, March 2002, INED-EUROREVES ";      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   char *alph[]={"a","a","b","c","d","e"}, str[4];  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       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);
   char z[1]="c", occ;  #endif
 #include <sys/time.h>    }
 #include <time.h>    return res;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  }
    
   /* long total_usecs;  /************** Inverse of matrix **************/
   struct timeval start_time, end_time;  void ludcmp(double **a, int n, int *indx, double *d) 
    { 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    int i,imax,j,k; 
     double big,dum,sum,temp; 
     double *vv; 
   printf("\n%s",version);   
   if(argc <=1){    vv=vector(1,n); 
     printf("\nEnter the parameter file name: ");    *d=1.0; 
     scanf("%s",pathtot);    for (i=1;i<=n;i++) { 
   }      big=0.0; 
   else{      for (j=1;j<=n;j++) 
     strcpy(pathtot,argv[1]);        if ((temp=fabs(a[i][j])) > big) big=temp; 
   }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      vv[i]=1.0/big; 
   /*cygwin_split_path(pathtot,path,optionfile);    } 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for (j=1;j<=n;j++) { 
   /* cutv(path,optionfile,pathtot,'\\');*/      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        a[i][j]=sum; 
   chdir(path);      } 
   replace(pathc,path);      big=0.0; 
       for (i=j;i<=n;i++) { 
 /*-------- arguments in the command line --------*/        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   strcpy(fileres,"r");          sum -= a[i][k]*a[k][j]; 
   strcat(fileres, optionfilefiname);        a[i][j]=sum; 
   strcat(fileres,".txt");    /* Other files have txt extension */        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
   /*---------arguments file --------*/          imax=i; 
         } 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      } 
     printf("Problem with optionfile %s\n",optionfile);      if (j != imax) { 
     goto end;        for (k=1;k<=n;k++) { 
   }          dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
   strcpy(filereso,"o");          a[j][k]=dum; 
   strcat(filereso,fileres);        } 
   if((ficparo=fopen(filereso,"w"))==NULL) {        *d = -(*d); 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        vv[imax]=vv[j]; 
   }      } 
       indx[j]=imax; 
   /* Reads comments: lines beginning with '#' */      if (a[j][j] == 0.0) a[j][j]=TINY; 
   while((c=getc(ficpar))=='#' && c!= EOF){      if (j != n) { 
     ungetc(c,ficpar);        dum=1.0/(a[j][j]); 
     fgets(line, MAXLINE, ficpar);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     puts(line);      } 
     fputs(line,ficparo);    } 
   }    free_vector(vv,1,n);  /* Doesn't work */
   ungetc(c,ficpar);  ;
   } 
   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);  
   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);  void lubksb(double **a, int n, int *indx, double b[]) 
   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);  { 
 while((c=getc(ficpar))=='#' && c!= EOF){    int i,ii=0,ip,j; 
     ungetc(c,ficpar);    double sum; 
     fgets(line, MAXLINE, ficpar);   
     puts(line);    for (i=1;i<=n;i++) { 
     fputs(line,ficparo);      ip=indx[i]; 
   }      sum=b[ip]; 
   ungetc(c,ficpar);      b[ip]=b[i]; 
        if (ii) 
            for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   covar=matrix(0,NCOVMAX,1,n);      else if (sum) ii=i; 
   cptcovn=0;      b[i]=sum; 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    } 
     for (i=n;i>=1;i--) { 
   ncovmodel=2+cptcovn;      sum=b[i]; 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        b[i]=sum/a[i][i]; 
   /* Read guess parameters */    } 
   /* Reads comments: lines beginning with '#' */  } 
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  void pstamp(FILE *fichier)
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     fputs(line,ficparo);  }
   }  
   ungetc(c,ficpar);  /************ Frequencies ********************/
    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[])
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  {  /* Some frequencies */
     for(i=1; i <=nlstate; i++)    
     for(j=1; j <=nlstate+ndeath-1; j++){    int i, m, jk, j1, bool, z1,j;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int first;
       fprintf(ficparo,"%1d%1d",i1,j1);    double ***freq; /* Frequencies */
       printf("%1d%1d",i,j);    double *pp, **prop;
       for(k=1; k<=ncovmodel;k++){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         fscanf(ficpar," %lf",&param[i][j][k]);    char fileresp[FILENAMELENGTH];
         printf(" %lf",param[i][j][k]);    
         fprintf(ficparo," %lf",param[i][j][k]);    pp=vector(1,nlstate);
       }    prop=matrix(1,nlstate,iagemin,iagemax+3);
       fscanf(ficpar,"\n");    strcpy(fileresp,"p");
       printf("\n");    strcat(fileresp,fileres);
       fprintf(ficparo,"\n");    if((ficresp=fopen(fileresp,"w"))==NULL) {
     }      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      exit(0);
     }
   p=param[1][1];    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
      j1=0;
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    j=cptcoveff;
     ungetc(c,ficpar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     fgets(line, MAXLINE, ficpar);  
     puts(line);    first=1;
     fputs(line,ficparo);  
   }    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
   ungetc(c,ficpar);    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
     /*    j1++; */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   for(i=1; i <=nlstate; i++){          scanf("%d", i);*/
     for(j=1; j <=nlstate+ndeath-1; j++){        for (i=-5; i<=nlstate+ndeath; i++)  
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       printf("%1d%1d",i,j);            for(m=iagemin; m <= iagemax+3; m++)
       fprintf(ficparo,"%1d%1d",i1,j1);              freq[i][jk][m]=0;
       for(k=1; k<=ncovmodel;k++){        
         fscanf(ficpar,"%le",&delti3[i][j][k]);        for (i=1; i<=nlstate; i++)  
         printf(" %le",delti3[i][j][k]);          for(m=iagemin; m <= iagemax+3; m++)
         fprintf(ficparo," %le",delti3[i][j][k]);            prop[i][m]=0;
       }        
       fscanf(ficpar,"\n");        dateintsum=0;
       printf("\n");        k2cpt=0;
       fprintf(ficparo,"\n");        for (i=1; i<=imx; i++) {
     }          bool=1;
   }          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
   delti=delti3[1][1];            for (z1=1; z1<=cptcoveff; z1++)       
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
   /* Reads comments: lines beginning with '#' */                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
   while((c=getc(ficpar))=='#' && c!= EOF){                bool=0;
     ungetc(c,ficpar);                /* 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", 
     fgets(line, MAXLINE, ficpar);                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
     puts(line);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
     fputs(line,ficparo);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
   }              } 
   ungetc(c,ficpar);          }
     
   matcov=matrix(1,npar,1,npar);          if (bool==1){
   for(i=1; i <=npar; i++){            for(m=firstpass; m<=lastpass; m++){
     fscanf(ficpar,"%s",&str);              k2=anint[m][i]+(mint[m][i]/12.);
     printf("%s",str);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     fprintf(ficparo,"%s",str);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for(j=1; j <=i; j++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fscanf(ficpar," %le",&matcov[i][j]);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       printf(" %.5le",matcov[i][j]);                if (m<lastpass) {
       fprintf(ficparo," %.5le",matcov[i][j]);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     fscanf(ficpar,"\n");                }
     printf("\n");                
     fprintf(ficparo,"\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   }                  dateintsum=dateintsum+k2;
   for(i=1; i <=npar; i++)                  k2cpt++;
     for(j=i+1;j<=npar;j++)                }
       matcov[i][j]=matcov[j][i];                /*}*/
                }
   printf("\n");          }
         } /* end i */
          
     /*-------- Rewriting paramater file ----------*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      strcpy(rfileres,"r");    /* "Rparameterfile */        pstamp(ficresp);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        if  (cptcovn>0) {
      strcat(rfileres,".");    /* */          fprintf(ficresp, "\n#********** Variable "); 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     if((ficres =fopen(rfileres,"w"))==NULL) {          fprintf(ficresp, "**********\n#");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(ficlog, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficres,"#%s\n",version);          fprintf(ficlog, "**********\n#");
            }
     /*-------- data file ----------*/        for(i=1; i<=nlstate;i++) 
     if((fic=fopen(datafile,"r"))==NULL)    {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       printf("Problem with datafile: %s\n", datafile);goto end;        fprintf(ficresp, "\n");
     }        
         for(i=iagemin; i <= iagemax+3; i++){
     n= lastobs;          if(i==iagemax+3){
     severity = vector(1,maxwav);            fprintf(ficlog,"Total");
     outcome=imatrix(1,maxwav+1,1,n);          }else{
     num=ivector(1,n);            if(first==1){
     moisnais=vector(1,n);              first=0;
     annais=vector(1,n);              printf("See log file for details...\n");
     moisdc=vector(1,n);            }
     andc=vector(1,n);            fprintf(ficlog,"Age %d", i);
     agedc=vector(1,n);          }
     cod=ivector(1,n);          for(jk=1; jk <=nlstate ; jk++){
     weight=vector(1,n);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              pp[jk] += freq[jk][m][i]; 
     mint=matrix(1,maxwav,1,n);          }
     anint=matrix(1,maxwav,1,n);          for(jk=1; jk <=nlstate ; jk++){
     s=imatrix(1,maxwav+1,1,n);            for(m=-1, pos=0; m <=0 ; m++)
     adl=imatrix(1,maxwav+1,1,n);                  pos += freq[jk][m][i];
     tab=ivector(1,NCOVMAX);            if(pp[jk]>=1.e-10){
     ncodemax=ivector(1,8);              if(first==1){
                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     i=1;              }
     while (fgets(line, MAXLINE, fic) != NULL)    {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       if ((i >= firstobs) && (i <=lastobs)) {            }else{
                      if(first==1)
         for (j=maxwav;j>=1;j--){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           strcpy(line,stra);            }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }          for(jk=1; jk <=nlstate ; jk++){
                    for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              pp[jk] += freq[jk][m][i];
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            pos += pp[jk];
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            posprop += prop[jk][i];
           }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          for(jk=1; jk <=nlstate ; jk++){
         for (j=ncov;j>=1;j--){            if(pos>=1.e-5){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);              if(first==1)
         }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         num[i]=atol(stra);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                    }else{
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              if(first==1)
           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;}*/                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         i=i+1;            }
       }            if( i <= iagemax){
     }              if(pos>=1.e-5){
     /* printf("ii=%d", ij);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
        scanf("%d",i);*/                /*probs[i][jk][j1]= pp[jk]/pos;*/
   imx=i-1; /* Number of individuals */                /*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 (i=1; i<=imx; i++){              else
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;            }
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          }
     }          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
     for (i=1; i<=imx; i++)            for(m=-1; m <=nlstate+ndeath; m++)
     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]));*/              if(freq[jk][m][i] !=0 ) {
               if(first==1)
   /* Calculation of the number of parameter from char model*/                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   Tvar=ivector(1,15);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   Tprod=ivector(1,15);              }
   Tvaraff=ivector(1,15);          if(i <= iagemax)
   Tvard=imatrix(1,15,1,2);            fprintf(ficresp,"\n");
   Tage=ivector(1,15);                if(first==1)
                printf("Others in log...\n");
   if (strlen(model) >1){          fprintf(ficlog,"\n");
     j=0, j1=0, k1=1, k2=1;        }
     j=nbocc(model,'+');        /*}*/
     j1=nbocc(model,'*');    }
     cptcovn=j+1;    dateintmean=dateintsum/k2cpt; 
     cptcovprod=j1;   
        fclose(ficresp);
        free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     strcpy(modelsav,model);    free_vector(pp,1,nlstate);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       printf("Error. Non available option model=%s ",model);    /* End of Freq */
       goto end;  }
     }  
      /************ Prevalence ********************/
     for(i=(j+1); i>=1;i--){  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       cutv(stra,strb,modelsav,'+');  {  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/       in each health status at the date of interview (if between dateprev1 and dateprev2).
       /*scanf("%d",i);*/       We still use firstpass and lastpass as another selection.
       if (strchr(strb,'*')) {    */
         cutv(strd,strc,strb,'*');   
         if (strcmp(strc,"age")==0) {    int i, m, jk, j1, bool, z1,j;
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    double **prop;
           Tvar[i]=atoi(stre);    double posprop; 
           cptcovage++;    double  y2; /* in fractional years */
             Tage[cptcovage]=i;    int iagemin, iagemax;
             /*printf("stre=%s ", stre);*/    int first; /** to stop verbosity which is redirected to log file */
         }  
         else if (strcmp(strd,"age")==0) {    iagemin= (int) agemin;
           cptcovprod--;    iagemax= (int) agemax;
           cutv(strb,stre,strc,'V');    /*pp=vector(1,nlstate);*/
           Tvar[i]=atoi(stre);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           cptcovage++;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           Tage[cptcovage]=i;    j1=0;
         }    
         else {    /*j=cptcoveff;*/
           cutv(strb,stre,strc,'V');    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           Tvar[i]=ncov+k1;    
           cutv(strb,strc,strd,'V');    first=1;
           Tprod[k1]=i;    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
           Tvard[k1][1]=atoi(strc);      /*for(i1=1; i1<=ncodemax[k1];i1++){
           Tvard[k1][2]=atoi(stre);        j1++;*/
           Tvar[cptcovn+k2]=Tvard[k1][1];        
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        for (i=1; i<=nlstate; i++)  
           for (k=1; k<=lastobs;k++)          for(m=iagemin; m <= iagemax+3; m++)
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            prop[i][m]=0.0;
           k1++;       
           k2=k2+2;        for (i=1; i<=imx; i++) { /* Each individual */
         }          bool=1;
       }          if  (cptcovn>0) {
       else {            for (z1=1; z1<=cptcoveff; z1++) 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        /*  scanf("%d",i);*/                bool=0;
       cutv(strd,strc,strb,'V');          } 
       Tvar[i]=atoi(strc);          if (bool==1) { 
       }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       strcpy(modelsav,stra);                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         scanf("%d",i);*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   printf("cptcovprod=%d ", cptcovprod);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   scanf("%d ",i);*/                  prop[s[m][i]][iagemax+3] += weight[i]; 
     fclose(fic);                } 
               }
     /*  if(mle==1){*/            } /* end selection of waves */
     if (weightopt != 1) { /* Maximisation without weights*/          }
       for(i=1;i<=n;i++) weight[i]=1.0;        }
     }        for(i=iagemin; i <= iagemax+3; i++){  
     /*-calculation of age at interview from date of interview and age at death -*/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     agev=matrix(1,maxwav,1,imx);            posprop += prop[jk][i]; 
           } 
    for (i=1; i<=imx; i++)          
      for(m=2; (m<= maxwav); m++)          for(jk=1; jk <=nlstate ; jk++){     
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            if( i <=  iagemax){ 
          anint[m][i]=9999;              if(posprop>=1.e-5){ 
          s[m][i]=-1;                probs[i][jk][j1]= prop[jk][i]/posprop;
        }              } else{
                    if(first==1){
     for (i=1; i<=imx; i++)  {                  first=0;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                  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]);
       for(m=1; (m<= maxwav); m++){                }
         if(s[m][i] >0){              }
           if (s[m][i] == nlstate+1) {            } 
             if(agedc[i]>0)          }/* end jk */ 
               if(moisdc[i]!=99 && andc[i]!=9999)        }/* end i */ 
               agev[m][i]=agedc[i];      /*} *//* end i1 */
             else {    } /* end j1 */
               if (andc[i]!=9999){    
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
               agev[m][i]=-1;    /*free_vector(pp,1,nlstate);*/
               }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
             }  }  /* End of prevalence */
           }  
           else if(s[m][i] !=9){ /* Should no more exist */  /************* Waves Concatenation ***************/
             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)  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)
               agev[m][i]=1;  {
             else if(agev[m][i] <agemin){    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
               agemin=agev[m][i];       Death is a valid wave (if date is known).
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       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]
             else if(agev[m][i] >agemax){       and mw[mi+1][i]. dh depends on stepm.
               agemax=agev[m][i];       */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    int i, mi, m;
             /*agev[m][i]=anint[m][i]-annais[i];*/    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             /*   agev[m][i] = age[i]+2*m;*/       double sum=0., jmean=0.;*/
           }    int first;
           else { /* =9 */    int j, k=0,jk, ju, jl;
             agev[m][i]=1;    double sum=0.;
             s[m][i]=-1;    first=0;
           }    jmin=100000;
         }    jmax=-1;
         else /*= 0 Unknown */    jmean=0.;
           agev[m][i]=1;    for(i=1; i<=imx; i++){
       }      mi=0;
          m=firstpass;
     }      while(s[m][i] <= nlstate){
     for (i=1; i<=imx; i++)  {        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       for(m=1; (m<= maxwav); m++){          mw[++mi][i]=m;
         if (s[m][i] > (nlstate+ndeath)) {        if(m >=lastpass)
           printf("Error: Wrong value in nlstate or ndeath\n");            break;
           goto end;        else
         }          m++;
       }      }/* end while */
     }      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
     free_vector(severity,1,maxwav);        mw[mi][i]=m;
     free_imatrix(outcome,1,maxwav+1,1,n);      }
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);      wav[i]=mi;
     /* free_matrix(mint,1,maxwav,1,n);      if(mi==0){
        free_matrix(anint,1,maxwav,1,n);*/        nbwarn++;
     free_vector(moisdc,1,n);        if(first==0){
     free_vector(andc,1,n);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
            }
     wav=ivector(1,imx);        if(first==1){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        }
          } /* end mi==0 */
     /* Concatenates waves */    } /* End individuals */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
       Tcode=ivector(1,100);        if (stepm <=0)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          dh[mi][i]=1;
       ncodemax[1]=1;        else{
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                  if (agedc[i] < 2*AGESUP) {
    codtab=imatrix(1,100,1,10);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
    h=0;              if(j==0) j=1;  /* Survives at least one month after exam */
    m=pow(2,cptcoveff);              else if(j<0){
                  nberr++;
    for(k=1;k<=cptcoveff; k++){                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      for(i=1; i <=(m/pow(2,k));i++){                j=1; /* Temporary Dangerous patch */
        for(j=1; j <= ncodemax[k]; j++){                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                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]);
            h++;                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
            if (h>m) h=1;codtab[h][k]=j;              }
          }              k=k+1;
        }              if (j >= jmax){
      }                jmax=j;
    }                ijmax=i;
               }
               if (j <= jmin){
    /*for(i=1; i <=m ;i++){                jmin=j;
      for(k=1; k <=cptcovn; k++){                ijmin=i;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);              }
      }              sum=sum+j;
      printf("\n");              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
    }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
    scanf("%d",i);*/            }
              }
    /* Calculates basic frequencies. Computes observed prevalence at single age          else{
        and prints on file fileres'p'. */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
      
                k=k+1;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if (j >= jmax) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              jmax=j;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              ijmax=i;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            else if (j <= jmin){
                    jmin=j;
     /* For Powell, parameters are in a vector p[] starting at p[1]              ijmin=i;
        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) */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     if(mle==1){            if(j<0){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              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]);
     /*--------- results files --------------*/            }
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);            sum=sum+j;
            }
           jk= j/stepm;
    jk=1;          jl= j -jk*stepm;
    fprintf(ficres,"# Parameters\n");          ju= j -(jk+1)*stepm;
    printf("# Parameters\n");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
    for(i=1,jk=1; i <=nlstate; i++){            if(jl==0){
      for(k=1; k <=(nlstate+ndeath); k++){              dh[mi][i]=jk;
        if (k != i)              bh[mi][i]=0;
          {            }else{ /* We want a negative bias in order to only have interpolation ie
            printf("%d%d ",i,k);                    * to avoid the price of an extra matrix product in likelihood */
            fprintf(ficres,"%1d%1d ",i,k);              dh[mi][i]=jk+1;
            for(j=1; j <=ncovmodel; j++){              bh[mi][i]=ju;
              printf("%f ",p[jk]);            }
              fprintf(ficres,"%f ",p[jk]);          }else{
              jk++;            if(jl <= -ju){
            }              dh[mi][i]=jk;
            printf("\n");              bh[mi][i]=jl;       /* bias is positive if real duration
            fprintf(ficres,"\n");                                   * is higher than the multiple of stepm and negative otherwise.
          }                                   */
      }            }
    }            else{
  if(mle==1){              dh[mi][i]=jk+1;
     /* Computing hessian and covariance matrix */              bh[mi][i]=ju;
     ftolhess=ftol; /* Usually correct */            }
     hesscov(matcov, p, npar, delti, ftolhess, func);            if(dh[mi][i]==0){
  }              dh[mi][i]=1; /* At least one step */
     fprintf(ficres,"# Scales\n");              bh[mi][i]=ju; /* At least one step */
     printf("# Scales\n");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
      for(i=1,jk=1; i <=nlstate; i++){            }
       for(j=1; j <=nlstate+ndeath; j++){          } /* end if mle */
         if (j!=i) {        }
           fprintf(ficres,"%1d%1d",i,j);      } /* end wave */
           printf("%1d%1d",i,j);    }
           for(k=1; k<=ncovmodel;k++){    jmean=sum/k;
             printf(" %.5e",delti[jk]);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
             fprintf(ficres," %.5e",delti[jk]);    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);
             jk++;   }
           }  
           printf("\n");  /*********** Tricode ****************************/
           fprintf(ficres,"\n");  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
         }  {
       }    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
      }    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
         * Boring subroutine which should only output nbcode[Tvar[j]][k]
     k=1;     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     fprintf(ficres,"# Covariance\n");     * nbcode[Tvar[j]][1]= 
     printf("# Covariance\n");    */
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
       i1=(i-1)/(ncovmodel*nlstate)+1;    int modmaxcovj=0; /* Modality max of covariates j */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    int cptcode=0; /* Modality max of covariates j */
       printf("%s%d%d",alph[k],i1,tab[i]);*/    int modmincovj=0; /* Modality min of covariates j */
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);  
       for(j=1; j<=i;j++){    cptcoveff=0; 
         fprintf(ficres," %.5e",matcov[i][j]);   
         printf(" %.5e",matcov[i][j]);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
       }    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
       fprintf(ficres,"\n");  
       printf("\n");    /* Loop on covariates without age and products */
       k++;    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
     }      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
                                     modality of this covariate Vj*/ 
     while((c=getc(ficpar))=='#' && c!= EOF){        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
       ungetc(c,ficpar);                                      * If product of Vn*Vm, still boolean *:
       fgets(line, MAXLINE, ficpar);                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
       puts(line);                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
       fputs(line,ficparo);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     }                                        modality of the nth covariate of individual i. */
     ungetc(c,ficpar);        if (ij > modmaxcovj)
            modmaxcovj=ij; 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);        else if (ij < modmincovj) 
              modmincovj=ij; 
     if (fage <= 2) {        if ((ij < -1) && (ij > NCOVMAX)){
       bage = agemin;          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
       fage = agemaxpar;          exit(1);
     }        }else
            Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        /* getting the maximum value of the modality of the covariate
             (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
     while((c=getc(ficpar))=='#' && c!= EOF){           female is 1, then modmaxcovj=1.*/
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     puts(line);      cptcode=modmaxcovj;
     fputs(line,ficparo);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   }     /*for (i=0; i<=cptcode; i++) {*/
   ungetc(c,ficpar);      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
          printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
              /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
   while((c=getc(ficpar))=='#' && c!= EOF){           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     ungetc(c,ficpar);      } /* Ndum[-1] number of undefined modalities */
     fgets(line, MAXLINE, ficpar);  
     puts(line);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     fputs(line,ficparo);      /* 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;
   ungetc(c,ficpar);         modmincovj=3; modmaxcovj = 7;
           There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
          which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;         variables V1_1 and V1_2.
    dateprev2=anprev2+mprev2/12.+jprev2/365.;         nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
   fscanf(ficpar,"pop_based=%d\n",&popbased);         nbcode[Tvar[j]][2]=1;
   fprintf(ficparo,"pop_based=%d\n",popbased);           nbcode[Tvar[j]][3]=2;
   fprintf(ficres,"pop_based=%d\n",popbased);        */
        ij=1; /* ij is similar to i but can jumps over null modalities */
   while((c=getc(ficpar))=='#' && c!= EOF){      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
     ungetc(c,ficpar);        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
     fgets(line, MAXLINE, ficpar);          /*recode from 0 */
     puts(line);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
     fputs(line,ficparo);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   }                                       k is a modality. If we have model=V1+V1*sex 
   ungetc(c,ficpar);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             ij++;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          if (ij > ncodemax[j]) break; 
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        }  /* 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*/  
 while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     fgets(line, MAXLINE, ficpar);    
     puts(line);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     fputs(line,ficparo);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   }     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
   ungetc(c,ficpar);     Ndum[ij]++; 
    } 
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);   ij=1;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);   for (i=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]);*/
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);     if((Ndum[i]!=0) && (i<=ncovcol)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
 /*------------ gnuplot -------------*/       Tvaraff[ij]=i; /*For printing (unclear) */
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);       ij++;
       }else
 /*------------ free_vector  -------------*/         Tvaraff[ij]=0;
  chdir(path);   }
     ij--;
  free_ivector(wav,1,imx);   cptcoveff=ij; /*Number of total covariates*/
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    }
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);  
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  /*********** Health Expectancies ****************/
  fclose(ficparo);  
  fclose(ficres);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
 /*--------- index.htm --------*/  {
     /* Health expectancies, no variances */
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);    int i, j, nhstepm, hstepm, h, nstepm;
     int nhstepma, nstepma; /* Decreasing with age */
      double age, agelim, hf;
   /*--------------- Prevalence limit --------------*/    double ***p3mat;
      double eip;
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);    pstamp(ficreseij);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fprintf(ficreseij,"# Age");
   }    for(i=1; i<=nlstate;i++){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      for(j=1; j<=nlstate;j++){
   fprintf(ficrespl,"#Prevalence limit\n");        fprintf(ficreseij," e%1d%1d ",i,j);
   fprintf(ficrespl,"#Age ");      }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      fprintf(ficreseij," e%1d. ",i);
   fprintf(ficrespl,"\n");    }
      fprintf(ficreseij,"\n");
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if(estepm < stepm){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf ("Problem %d lower than %d\n",estepm, stepm);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    else  hstepm=estepm;   
   k=0;    /* We compute the life expectancy from trapezoids spaced every estepm months
   agebase=agemin;     * This is mainly to measure the difference between two models: for example
   agelim=agemaxpar;     * if stepm=24 months pijx are given only every 2 years and by summing them
   ftolpl=1.e-10;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   i1=cptcoveff;     * progression in between and thus overestimating or underestimating according
   if (cptcovn < 1){i1=1;}     * 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
   for(cptcov=1;cptcov<=i1;cptcov++){     * to compare the new estimate of Life expectancy with the same linear 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     * hypothesis. A more precise result, taking into account a more precise
         k=k+1;     * curvature will be obtained if estepm is as small as stepm. */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");    /* For example we decided to compute the life expectancy with the smallest unit */
         for(j=1;j<=cptcoveff;j++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficrespl,"******\n");       nstepm is the number of stepm from age to agelin. 
               Look at hpijx to understand the reason of that which relies in memory size
         for (age=agebase; age<=agelim; age++){       and note for a fixed period like estepm months */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           fprintf(ficrespl,"%.0f",age );       survival function given by stepm (the optimization length). Unfortunately it
           for(i=1; i<=nlstate;i++)       means that if the survival funtion is printed only each two years of age and if
           fprintf(ficrespl," %.5f", prlim[i][i]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           fprintf(ficrespl,"\n");       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 */ 
     }  
   fclose(ficrespl);    agelim=AGESUP;
     /* If stepm=6 months */
   /*------------- h Pij x at various ages ------------*/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  /* nhstepm age range expressed in number of stepm */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   printf("Computing pij: result on file '%s' \n", filerespij);    /* if (stepm >= YEARM) hstepm=1;*/
      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*if (stepm<=24) stepsize=2;*/  
     for (age=bage; age<=fage; age ++){ 
   agelim=AGESUP;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   hstepm=stepsize*YEARM; /* Every year of age */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){      /* If stepm=6 months */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      /* Computed by stepm unit matrices, product of hstepma matrices, stored
       k=k+1;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
         fprintf(ficrespij,"\n#****** ");      
         for(j=1;j<=cptcoveff;j++)      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      
         fprintf(ficrespij,"******\n");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
              
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      printf("%d|",(int)age);fflush(stdout);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* Computing expectancies */
           oldm=oldms;savm=savms;      for(i=1; i<=nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(j=1; j<=nlstate;j++)
           fprintf(ficrespij,"# Age");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           for(i=1; i<=nlstate;i++)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             for(j=1; j<=nlstate+ndeath;j++)            
               fprintf(ficrespij," %1d-%1d",i,j);            /* 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(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){          }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)      fprintf(ficreseij,"%3.0f",age );
               for(j=1; j<=nlstate+ndeath;j++)      for(i=1; i<=nlstate;i++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        eip=0;
             fprintf(ficrespij,"\n");        for(j=1; j<=nlstate;j++){
           }          eip +=eij[i][j][(int)age];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
           fprintf(ficrespij,"\n");        }
         }        fprintf(ficreseij,"%9.4f", eip );
     }      }
   }      fprintf(ficreseij,"\n");
       
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficrespij);    printf("\n");
     fprintf(ficlog,"\n");
     
   /*---------- Forecasting ------------------*/  }
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
     free_matrix(mint,1,maxwav,1,n);  {
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    /* Covariances of health expectancies eij and of total life expectancies according
     free_vector(weight,1,n);}     to initial status i, ei. .
   else{    */
     erreur=108;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     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);    int nhstepma, nstepma; /* Decreasing with age */
   }    double age, agelim, hf;
      double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
   /*---------- Health expectancies and variances ------------*/    double *xp, *xm;
     double **gp, **gm;
   strcpy(filerest,"t");    double ***gradg, ***trgradg;
   strcat(filerest,fileres);    int theta;
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    double eip, vip;
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
   strcpy(filerese,"e");    dnewm=matrix(1,nlstate*nlstate,1,npar);
   strcat(filerese,fileres);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    pstamp(ficresstdeij);
   }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
  strcpy(fileresv,"v");      for(j=1; j<=nlstate;j++)
   strcat(fileresv,fileres);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      fprintf(ficresstdeij," e%1d. ",i);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    }
   }    fprintf(ficresstdeij,"\n");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
     pstamp(ficrescveij);
   k=0;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficrescveij,"# Age");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(i=1; i<=nlstate;i++)
       k=k+1;      for(j=1; j<=nlstate;j++){
       fprintf(ficrest,"\n#****** ");        cptj= (j-1)*nlstate+i;
       for(j=1;j<=cptcoveff;j++)        for(i2=1; i2<=nlstate;i2++)
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(j2=1; j2<=nlstate;j2++){
       fprintf(ficrest,"******\n");            cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
       fprintf(ficreseij,"\n#****** ");              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       for(j=1;j<=cptcoveff;j++)          }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      }
       fprintf(ficreseij,"******\n");    fprintf(ficrescveij,"\n");
     
       fprintf(ficresvij,"\n#****** ");    if(estepm < stepm){
       for(j=1;j<=cptcoveff;j++)      printf ("Problem %d lower than %d\n",estepm, stepm);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    }
       fprintf(ficresvij,"******\n");    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     * This is mainly to measure the difference between two models: for example
       oldm=oldms;savm=savms;     * if stepm=24 months pijx are given only every 2 years and by summing them
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);       * we are calculating an estimate of the Life Expectancy assuming a linear 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     * progression in between and thus overestimating or underestimating according
       oldm=oldms;savm=savms;     * to the curvature of the survival function. If, for the same date, we 
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     * 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. */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficrest,"\n");    /* 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 
       epj=vector(1,nlstate+1);       nstepm is the number of stepm from age to agelin. 
       for(age=bage; age <=fage ;age++){       Look at hpijx to understand the reason of that which relies in memory size
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       and note for a fixed period like estepm months */
         if (popbased==1) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           for(i=1; i<=nlstate;i++)       survival function given by stepm (the optimization length). Unfortunately it
             prlim[i][i]=probs[(int)age][i][k];       means that if the survival funtion is printed only each two years of age and if
         }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               results. So we changed our mind and took the option of the best precision.
         fprintf(ficrest," %4.0f",age);    */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    /* If stepm=6 months */
           }    /* nhstepm age range expressed in number of stepm */
           epj[nlstate+1] +=epj[j];    agelim=AGESUP;
         }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
         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," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));    
         for(j=1;j <=nlstate;j++){    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         fprintf(ficrest,"\n");    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 ++){ 
   fclose(ficreseij);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   fclose(ficresvij);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fclose(ficrest);      /* if (stepm >= YEARM) hstepm=1;*/
   fclose(ficpar);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   free_vector(epj,1,nlstate+1);  
        /* If stepm=6 months */
   /*------- Variance limit prevalence------*/        /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   strcpy(fileresvpl,"vpl");      
   strcat(fileresvpl,fileres);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      /* Computing  Variances of health expectancies */
     exit(0);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   }         decrease memory allocation */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
   k=0;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   for(cptcov=1;cptcov<=i1;cptcov++){          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
       k=k+1;        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       fprintf(ficresvpl,"\n#****** ");        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<= nlstate; j++){
       fprintf(ficresvpl,"******\n");          for(i=1; i<=nlstate; i++){
                  for(h=0; h<=nhstepm-1; h++){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
       oldm=oldms;savm=savms;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            }
     }          }
  }        }
        
   fclose(ficresvpl);        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
   /*---------- End : free ----------------*/            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          }
        }/* End theta */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      
        for(h=0; h<=nhstepm-1; h++)
          for(j=1; j<=nlstate*nlstate;j++)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          for(theta=1; theta <=npar; theta++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            trgradg[h][j][theta]=gradg[h][theta][j];
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
         for(ij=1;ij<=nlstate*nlstate;ij++)
   free_matrix(matcov,1,npar,1,npar);        for(ji=1;ji<=nlstate*nlstate;ji++)
   free_vector(delti,1,npar);          varhe[ij][ji][(int)age] =0.;
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   if(erreur >0)       for(h=0;h<=nhstepm-1;h++){
     printf("End of Imach with error %d\n",erreur);        for(k=0;k<=nhstepm-1;k++){
   else   printf("End of Imach\n");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
            for(ij=1;ij<=nlstate*nlstate;ij++)
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/            for(ji=1;ji<=nlstate*nlstate;ji++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   /*------ End -----------*/        }
       }
   
  end:      /* Computing expectancies */
 #ifdef windows      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   /* chdir(pathcd);*/      for(i=1; i<=nlstate;i++)
 #endif        for(j=1; j<=nlstate;j++)
  /*system("wgnuplot graph.plt");*/          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
  /*system("../gp37mgw/wgnuplot graph.plt");*/            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
  /*system("cd ../gp37mgw");*/            
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            /* 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]);*/
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");          }
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);      fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
 #ifdef windows        eip=0.;
   while (z[0] != 'q') {        vip=0.;
     chdir(path);        for(j=1; j<=nlstate;j++){
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          eip += eij[i][j][(int)age];
     scanf("%s",z);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     if (z[0] == 'c') system("./imach");            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     else if (z[0] == 'e') {          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       chdir(path);        }
       system(optionfilehtm);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     }      }
     else if (z[0] == 'q') exit(0);      fprintf(ficresstdeij,"\n");
   }  
 #endif      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 __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #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
   
   #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__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         /*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
           k=k+1; 
       /* for (k=1; k <= (int) pow(2,cptcoveff); k++){*/
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             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);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
               fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         /*}*/
       }
   }
   
   
   /***********************************************/
   /**************** 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 */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       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.1.33  
changed lines
  Added in v.1.180


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>