Diff for /imach/src/imach.c between versions 1.28 and 1.179

version 1.28, 2002/03/01 17:56:23 version 1.179, 2015/01/04 09:57:06
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.179  2015/01/04 09:57:06  brouard
      Summary: back to OS/X
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.178  2015/01/04 09:35:48  brouard
   first survey ("cross") where individuals from different ages are    *** empty log message ***
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.177  2015/01/03 18:40:56  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: Still testing ilc32 on OSX
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.176  2015/01/03 16:45:04  brouard
   model. More health states you consider, more time is necessary to reach the    *** empty log message ***
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.175  2015/01/03 16:33:42  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 1.174  2015/01/03 16:15:49  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Summary: Still in cross-compilation
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.173  2015/01/03 12:06:26  brouard
   you to do it.  More covariates you add, slower the    Summary: trying to detect cross-compilation
   convergence.  
     Revision 1.172  2014/12/27 12:07:47  brouard
   The advantage of this computer programme, compared to a simple    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.171  2014/12/23 13:26:59  brouard
   intermediate interview, the information is lost, but taken into    Summary: Back from Visual C
   account using an interpolation or extrapolation.    
     Still problem with utsname.h on Windows
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.170  2014/12/23 11:17:12  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: Cleaning some \%% back to %%
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.169  2014/12/22 23:08:31  brouard
   hPijx.    Summary: 0.98p
   
   Also this programme outputs the covariance matrix of the parameters but also    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.168  2014/12/22 15:17:42  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Summary: update
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.167  2014/12/22 13:50:56  brouard
   from the European Union.    Summary: Testing uname and compiler version and if compiled 32 or 64
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Testing on Linux 64
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.166  2014/12/22 11:40:47  brouard
      *** empty log message ***
 #include <math.h>  
 #include <stdio.h>    Revision 1.165  2014/12/16 11:20:36  brouard
 #include <stdlib.h>    Summary: After compiling on Visual C
 #include <unistd.h>  
     * imach.c (Module): Merging 1.61 to 1.162
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Revision 1.164  2014/12/16 10:52:11  brouard
 #define FILENAMELENGTH 80    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 /*#define DEBUG*/  
 #define windows    * imach.c (Module): Merging 1.61 to 1.162
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.163  2014/12/16 10:30:11  brouard
     * 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 1.162  2014/09/25 11:43:39  brouard
     Summary: temporary backup 0.99!
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.1  2014/09/16 11:06:58  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Summary: With some code (wrong) for nlopt
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Author:
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.161  2014/09/15 20:41:41  brouard
 #define AGEBASE 40    Summary: Problem with macro SQR on Intel compiler
   
     Revision 1.160  2014/09/02 09:24:05  brouard
 int erreur; /* Error number */    *** empty log message ***
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.159  2014/09/01 10:34:10  brouard
 int npar=NPARMAX;    Summary: WIN32
 int nlstate=2; /* Number of live states */    Author: Brouard
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.158  2014/08/27 17:11:51  brouard
 int popbased=0;    *** empty log message ***
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.157  2014/08/27 16:26:55  brouard
 int maxwav; /* Maxim number of waves */    Summary: Preparing windows Visual studio version
 int jmin, jmax; /* min, max spacing between 2 waves */    Author: Brouard
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    In order to compile on Visual studio, time.h is now correct and time_t
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    and tm struct should be used. difftime should be used but sometimes I
 double jmean; /* Mean space between 2 waves */    just make the differences in raw time format (time(&now).
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Trying to suppress #ifdef LINUX
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Add xdg-open for __linux in order to open default browser.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.156  2014/08/25 20:10:10  brouard
 FILE *ficreseij;    *** empty log message ***
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.155  2014/08/25 18:32:34  brouard
   char fileresv[FILENAMELENGTH];    Summary: New compile, minor changes
  FILE  *ficresvpl;    Author: Brouard
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.154  2014/06/20 17:32:08  brouard
 #define NR_END 1    Summary: Outputs now all graphs of convergence to period prevalence
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
 #define NRANSI    Author: Brouard
 #define ITMAX 200  
     Revision 1.152  2014/06/18 17:54:09  brouard
 #define TOL 2.0e-4    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
 #define CGOLD 0.3819660    Revision 1.151  2014/06/18 16:43:30  brouard
 #define ZEPS 1.0e-10    *** empty log message ***
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.150  2014/06/18 16:42:35  brouard
 #define GOLD 1.618034    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 #define GLIMIT 100.0    Author: brouard
 #define TINY 1.0e-20  
     Revision 1.149  2014/06/18 15:51:14  brouard
 static double maxarg1,maxarg2;    Summary: Some fixes in parameter files errors
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Author: Nicolas Brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.148  2014/06/17 17:38:48  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Summary: Nothing new
 #define rint(a) floor(a+0.5)    Author: Brouard
   
 static double sqrarg;    Just a new packaging for OS/X version 0.98nS
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
 int imx;  
 int stepm;    Revision 1.146  2014/06/16 10:20:28  brouard
 /* Stepm, step in month: minimum step interpolation*/    Summary: Merge
     Author: Brouard
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Merge, before building revised version.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.145  2014/06/10 21:23:15  brouard
 double dateintmean=0;    Summary: Debugging with valgrind
     Author: Nicolas Brouard
 double *weight;  
 int **s; /* Status */    Lot of changes in order to output the results with some covariates
 double *agedc, **covar, idx;    After the Edimburgh REVES conference 2014, it seems mandatory to
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    improve the code.
     No more memory valgrind error but a lot has to be done in order to
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    continue the work of splitting the code into subroutines.
 double ftolhess; /* Tolerance for computing hessian */    Also, decodemodel has been improved. Tricode is still not
     optimal. nbcode should be improved. Documentation has been added in
 /**************** split *************************/    the source code.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.143  2014/01/26 09:45:38  brouard
    char *s;                             /* pointer */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
    int  l1, l2;                         /* length counters */  
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    l1 = strlen( path );                 /* length of path */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.142  2014/01/26 03:57:36  brouard
    s = strrchr( path, '\\' );           /* find last / */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 #else  
    s = strrchr( path, '/' );            /* find last / */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.141  2014/01/26 02:42:01  brouard
 #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 1.140  2011/09/02 10:37:54  brouard
       if ( getwd( dirc ) == NULL ) {    Summary: times.h is ok with mingw32 now.
 #else  
       extern char       *getcwd( );    Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.138  2010/04/30 18:19:40  brouard
       }    *** empty log message ***
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.137  2010/04/29 18:11:38  brouard
       s++;                              /* after this, the filename */    (Module): Checking covariates for more complex models
       l2 = strlen( s );                 /* length of filename */    than V1+V2. A lot of change to be done. Unstable.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.136  2010/04/26 20:30:53  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): merging some libgsl code. Fixing computation
       dirc[l1-l2] = 0;                  /* add zero */    of likelione (using inter/intrapolation if mle = 0) in order to
    }    get same likelihood as if mle=1.
    l1 = strlen( dirc );                 /* length of directory */    Some cleaning of code and comments added.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.135  2009/10/29 15:33:14  brouard
 #else    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.134  2009/10/29 13:18:53  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 1.133  2009/07/06 10:21:25  brouard
    l1= strlen( name);    just nforces
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.132  2009/07/06 08:22:05  brouard
    finame[l1-l2]= 0;    Many tings
    return( 0 );                         /* we're done */  
 }    Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
   
 /******************************************/    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
 void replace(char *s, char*t)    lot of cleaning with variables initialized to 0. Trying to make
 {    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   int i;  
   int lg=20;    Revision 1.129  2007/08/31 13:49:27  lievre
   i=0;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.128  2006/06/30 13:02:05  brouard
     (s[i] = t[i]);    (Module): Clarifications on computing e.j
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.127  2006/04/28 18:11:50  brouard
 }    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 int nbocc(char *s, char occ)    loop. Now we define nhstepma in the age loop.
 {    (Module): In order to speed up (in case of numerous covariates) we
   int i,j=0;    compute health expectancies (without variances) in a first step
   int lg=20;    and then all the health expectancies with variances or standard
   i=0;    deviation (needs data from the Hessian matrices) which slows the
   lg=strlen(s);    computation.
   for(i=0; i<= lg; i++) {    In the future we should be able to stop the program is only health
   if  (s[i] == occ ) j++;    expectancies and graph are needed without standard deviations.
   }  
   return j;    Revision 1.126  2006/04/28 17:23:28  brouard
 }    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 void cutv(char *u,char *v, char*t, char occ)    loop. Now we define nhstepma in the age loop.
 {    Version 0.98h
   int i,lg,j,p=0;  
   i=0;    Revision 1.125  2006/04/04 15:20:31  lievre
   for(j=0; j<=strlen(t)-1; j++) {    Errors in calculation of health expectancies. Age was not initialized.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Forecasting file added.
   }  
     Revision 1.124  2006/03/22 17:13:53  lievre
   lg=strlen(t);    Parameters are printed with %lf instead of %f (more numbers after the comma).
   for(j=0; j<p; j++) {    The log-likelihood is printed in the log file
     (u[j] = t[j]);  
   }    Revision 1.123  2006/03/20 10:52:43  brouard
      u[p]='\0';    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    * imach.c (Module): Weights can have a decimal point as for
   }    English (a comma might work with a correct LC_NUMERIC environment,
 }    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 /********************** nrerror ********************/    1.
     Version 0.98g
 void nrerror(char error_text[])  
 {    Revision 1.122  2006/03/20 09:45:41  brouard
   fprintf(stderr,"ERREUR ...\n");    (Module): Weights can have a decimal point as for
   fprintf(stderr,"%s\n",error_text);    English (a comma might work with a correct LC_NUMERIC environment,
   exit(1);    otherwise the weight is truncated).
 }    Modification of warning when the covariates values are not 0 or
 /*********************** vector *******************/    1.
 double *vector(int nl, int nh)    Version 0.98g
 {  
   double *v;    Revision 1.121  2006/03/16 17:45:01  lievre
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    * imach.c (Module): Comments concerning covariates added
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    * imach.c (Module): refinements in the computation of lli if
 }    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.120  2006/03/16 15:10:38  lievre
 {    (Module): refinements in the computation of lli if
   free((FREE_ARG)(v+nl-NR_END));    status=-2 in order to have more reliable computation if stepm is
 }    not 1 month. Version 0.98f
   
 /************************ivector *******************************/    Revision 1.119  2006/03/15 17:42:26  brouard
 int *ivector(long nl,long nh)    (Module): Bug if status = -2, the loglikelihood was
 {    computed as likelihood omitting the logarithm. Version O.98e
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.118  2006/03/14 18:20:07  brouard
   if (!v) nrerror("allocation failure in ivector");    (Module): varevsij Comments added explaining the second
   return v-nl+NR_END;    table of variances if popbased=1 .
 }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 /******************free ivector **************************/    (Module): Version 0.98d
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.117  2006/03/14 17:16:22  brouard
   free((FREE_ARG)(v+nl-NR_END));    (Module): varevsij Comments added explaining the second
 }    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /******************* imatrix *******************************/    (Module): Function pstamp added
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Module): Version 0.98d
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Revision 1.116  2006/03/06 10:29:27  brouard
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Module): Variance-covariance wrong links and
   int **m;    varian-covariance of ej. is needed (Saito).
    
   /* allocate pointers to rows */    Revision 1.115  2006/02/27 12:17:45  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Module): One freematrix added in mlikeli! 0.98c
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.114  2006/02/26 12:57:58  brouard
   m -= nrl;    (Module): Some improvements in processing parameter
      filename with strsep.
    
   /* allocate rows and set pointers to them */    Revision 1.113  2006/02/24 14:20:24  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    (Module): Memory leaks checks with valgrind and:
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    datafile was not closed, some imatrix were not freed and on matrix
   m[nrl] += NR_END;    allocation too.
   m[nrl] -= ncl;  
      Revision 1.112  2006/01/30 09:55:26  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    
   /* return pointer to array of pointers to rows */    Revision 1.111  2006/01/25 20:38:18  brouard
   return m;    (Module): Lots of cleaning and bugs added (Gompertz)
 }    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.110  2006/01/25 00:51:50  brouard
       int **m;    (Module): Lots of cleaning and bugs added (Gompertz)
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.109  2006/01/24 19:37:15  brouard
 {    (Module): Comments (lines starting with a #) are allowed in data.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.108  2006/01/19 18:05:42  lievre
 }    Gnuplot problem appeared...
     To be fixed
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.107  2006/01/19 16:20:37  brouard
 {    Test existence of gnuplot in imach path
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.105  2006/01/05 20:23:19  lievre
   m += NR_END;    *** empty log message ***
   m -= nrl;  
     Revision 1.104  2005/09/30 16:11:43  lievre
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): sump fixed, loop imx fixed, and simplifications.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): If the status is missing at the last wave but we know
   m[nrl] += NR_END;    that the person is alive, then we can code his/her status as -2
   m[nrl] -= ncl;    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   return m;    the healthy state at last known wave). Version is 0.98
 }  
     Revision 1.103  2005/09/30 15:54:49  lievre
 /*************************free matrix ************************/    (Module): sump fixed, loop imx fixed, and simplifications.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.102  2004/09/15 17:31:30  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Add the possibility to read data file including tab characters.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Revision 1.100  2004/07/12 18:29:06  brouard
 {    Add version for Mac OS X. Just define UNIX in Makefile
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.98  2004/05/16 15:05:56  brouard
   m += NR_END;    New version 0.97 . First attempt to estimate force of mortality
   m -= nrl;    directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    This is the basic analysis of mortality and should be done before any
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    other analysis, in order to test if the mortality estimated from the
   m[nrl] += NR_END;    cross-longitudinal survey is different from the mortality estimated
   m[nrl] -= ncl;    from other sources like vital statistic data.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    The same imach parameter file can be used but the option for mle should be -3.
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Agnès, who wrote this part of the code, tried to keep most of the
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    former routines in order to include the new code within the former code.
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    The output is very simple: only an estimate of the intercept and of
   for (j=ncl+1; j<=nch; j++)    the slope with 95% confident intervals.
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Current limitations:
   for (i=nrl+1; i<=nrh; i++) {    A) Even if you enter covariates, i.e. with the
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     for (j=ncl+1; j<=nch; j++)    B) There is no computation of Life Expectancy nor Life Table.
       m[i][j]=m[i][j-1]+nlay;  
   }    Revision 1.97  2004/02/20 13:25:42  lievre
   return m;    Version 0.96d. Population forecasting command line is (temporarily)
 }    suppressed.
   
 /*************************free ma3x ************************/    Revision 1.96  2003/07/15 15:38:55  brouard
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 {    rewritten within the same printf. Workaround: many printfs.
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.95  2003/07/08 07:54:34  brouard
   free((FREE_ARG)(m+nrl-NR_END));    * imach.c (Repository):
 }    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
 /***************** f1dim *************************/  
 extern int ncom;    Revision 1.94  2003/06/27 13:00:02  brouard
 extern double *pcom,*xicom;    Just cleaning
 extern double (*nrfunc)(double []);  
      Revision 1.93  2003/06/25 16:33:55  brouard
 double f1dim(double x)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   int j;    (Module): Version 0.96b
   double f;  
   double *xt;    Revision 1.92  2003/06/25 16:30:45  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
   xt=vector(1,ncom);    exist so I changed back to asctime which exists.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    Revision 1.91  2003/06/25 15:30:29  brouard
   free_vector(xt,1,ncom);    * imach.c (Repository): Duplicated warning errors corrected.
   return f;    (Repository): Elapsed time after each iteration is now output. It
 }    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 /*****************brent *************************/    concerning matrix of covariance. It has extension -cov.htm.
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {    Revision 1.90  2003/06/24 12:34:15  brouard
   int iter;    (Module): Some bugs corrected for windows. Also, when
   double a,b,d,etemp;    mle=-1 a template is output in file "or"mypar.txt with the design
   double fu,fv,fw,fx;    of the covariance matrix to be input.
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    Revision 1.89  2003/06/24 12:30:52  brouard
   double e=0.0;    (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
   a=(ax < cx ? ax : cx);    of the covariance matrix to be input.
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.88  2003/06/23 17:54:56  brouard
   fw=fv=fx=(*f)(x);    * 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.
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    Revision 1.87  2003/06/18 12:26:01  brouard
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    Version 0.96
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    Revision 1.86  2003/06/17 20:04:08  brouard
 #ifdef DEBUG    (Module): Change position of html and gnuplot routines and added
     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);    routine fileappend.
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    Revision 1.85  2003/06/17 13:12:43  brouard
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    * imach.c (Repository): Check when date of death was earlier that
       *xmin=x;    current date of interview. It may happen when the death was just
       return fx;    prior to the death. In this case, dh was negative and likelihood
     }    was wrong (infinity). We still send an "Error" but patch by
     ftemp=fu;    assuming that the date of death was just one stepm after the
     if (fabs(e) > tol1) {    interview.
       r=(x-w)*(fx-fv);    (Repository): Because some people have very long ID (first column)
       q=(x-v)*(fx-fw);    we changed int to long in num[] and we added a new lvector for
       p=(x-v)*q-(x-w)*r;    memory allocation. But we also truncated to 8 characters (left
       q=2.0*(q-r);    truncation)
       if (q > 0.0) p = -p;    (Repository): No more line truncation errors.
       q=fabs(q);  
       etemp=e;    Revision 1.84  2003/06/13 21:44:43  brouard
       e=d;    * imach.c (Repository): Replace "freqsummary" at a correct
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    place. It differs from routine "prevalence" which may be called
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    many times. Probs is memory consuming and must be used with
       else {    parcimony.
         d=p/q;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)    Revision 1.83  2003/06/10 13:39:11  lievre
           d=SIGN(tol1,xm-x);    *** empty log message ***
       }  
     } else {    Revision 1.82  2003/06/05 15:57:20  brouard
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    Add log in  imach.c and  fullversion number is now printed.
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  */
     fu=(*f)(u);  /*
     if (fu <= fx) {     Interpolated Markov Chain
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)    Short summary of the programme:
         SHFT(fv,fw,fx,fu)    
         } else {    This program computes Healthy Life Expectancies from
           if (u < x) a=u; else b=u;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
           if (fu <= fw || w == x) {    first survey ("cross") where individuals from different ages are
             v=w;    interviewed on their health status or degree of disability (in the
             w=u;    case of a health survey which is our main interest) -2- at least a
             fv=fw;    second wave of interviews ("longitudinal") which measure each change
             fw=fu;    (if any) in individual health status.  Health expectancies are
           } else if (fu <= fv || v == x || v == w) {    computed from the time spent in each health state according to a
             v=u;    model. More health states you consider, more time is necessary to reach the
             fv=fu;    Maximum Likelihood of the parameters involved in the model.  The
           }    simplest model is the multinomial logistic model where pij is the
         }    probability to be observed in state j at the second wave
   }    conditional to be observed in state i at the first wave. Therefore
   nrerror("Too many iterations in brent");    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   *xmin=x;    'age' is age and 'sex' is a covariate. If you want to have a more
   return fx;    complex model than "constant and age", you should modify the program
 }    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 /****************** mnbrak ***********************/    convergence.
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    The advantage of this computer programme, compared to a simple
             double (*func)(double))    multinomial logistic model, is clear when the delay between waves is not
 {    identical for each individual. Also, if a individual missed an
   double ulim,u,r,q, dum;    intermediate interview, the information is lost, but taken into
   double fu;    account using an interpolation or extrapolation.  
    
   *fa=(*func)(*ax);    hPijx is the probability to be observed in state i at age x+h
   *fb=(*func)(*bx);    conditional to the observed state i at age x. The delay 'h' can be
   if (*fb > *fa) {    split into an exact number (nh*stepm) of unobserved intermediate
     SHFT(dum,*ax,*bx,dum)    states. This elementary transition (by month, quarter,
       SHFT(dum,*fb,*fa,dum)    semester or year) is modelled as a multinomial logistic.  The hPx
       }    matrix is simply the matrix product of nh*stepm elementary matrices
   *cx=(*bx)+GOLD*(*bx-*ax);    and the contribution of each individual to the likelihood is simply
   *fc=(*func)(*cx);    hPijx.
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);    Also this programme outputs the covariance matrix of the parameters but also
     q=(*bx-*cx)*(*fb-*fa);    of the life expectancies. It also computes the period (stable) prevalence. 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     ulim=(*bx)+GLIMIT*(*cx-*bx);             Institut national d'études démographiques, Paris.
     if ((*bx-u)*(u-*cx) > 0.0) {    This software have been partly granted by Euro-REVES, a concerted action
       fu=(*func)(u);    from the European Union.
     } else if ((*cx-u)*(u-ulim) > 0.0) {    It is copyrighted identically to a GNU software product, ie programme and
       fu=(*func)(u);    software can be distributed freely for non commercial use. Latest version
       if (fu < *fc) {    can be accessed at http://euroreves.ined.fr/imach .
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
           }    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    
       u=ulim;    **********************************************************************/
       fu=(*func)(u);  /*
     } else {    main
       u=(*cx)+GOLD*(*cx-*bx);    read parameterfile
       fu=(*func)(u);    read datafile
     }    concatwav
     SHFT(*ax,*bx,*cx,u)    freqsummary
       SHFT(*fa,*fb,*fc,fu)    if (mle >= 1)
       }      mlikeli
 }    print results files
     if mle==1 
 /*************** linmin ************************/       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 int ncom;        begin-prev-date,...
 double *pcom,*xicom;    open gnuplot file
 double (*nrfunc)(double []);    open html file
      period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 {                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   double brent(double ax, double bx, double cx,      freexexit2 possible for memory heap.
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);    h Pij x                         | pij_nom  ficrestpij
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
               double *fc, double (*func)(double));         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   int j;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   double xx,xmin,bx,ax;  
   double fx,fb,fa;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
           1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   ncom=n;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   pcom=vector(1,n);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   xicom=vector(1,n);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   nrfunc=func;  
   for (j=1;j<=n;j++) {    forecasting if prevfcast==1 prevforecast call prevalence()
     pcom[j]=p[j];    health expectancies
     xicom[j]=xi[j];    Variance-covariance of DFLE
   }    prevalence()
   ax=0.0;     movingaverage()
   xx=1.0;    varevsij() 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    if popbased==1 varevsij(,popbased)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    total life expectancies
 #ifdef DEBUG    Variance of period (stable) prevalence
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);   end
 #endif  */
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  #define POWELL /* Instead of NLOPT */
     p[j] += xi[j];  
   }  #include <math.h>
   free_vector(xicom,1,n);  #include <stdio.h>
   free_vector(pcom,1,n);  #include <stdlib.h>
 }  #include <string.h>
   
 /*************** powell ************************/  #ifdef _WIN32
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #include <io.h>
             double (*func)(double []))  #include <windows.h>
 {  #include <tchar.h>
   void linmin(double p[], double xi[], int n, double *fret,  #else
               double (*func)(double []));  #include <unistd.h>
   int i,ibig,j;  #endif
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  #include <limits.h>
   double *xits;  #include <sys/types.h>
   pt=vector(1,n);  
   ptt=vector(1,n);  #if defined(__GNUC__)
   xit=vector(1,n);  #include <sys/utsname.h> /* Doesn't work on Windows */
   xits=vector(1,n);  #endif
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  #include <sys/stat.h>
   for (*iter=1;;++(*iter)) {  #include <errno.h>
     fp=(*fret);  /* extern int errno; */
     ibig=0;  
     del=0.0;  /* #ifdef LINUX */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /* #include <time.h> */
     for (i=1;i<=n;i++)  /* #include "timeval.h" */
       printf(" %d %.12f",i, p[i]);  /* #else */
     printf("\n");  /* #include <sys/time.h> */
     for (i=1;i<=n;i++) {  /* #endif */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  #include <time.h>
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  #ifdef GSL
 #endif  #include <gsl/gsl_errno.h>
       printf("%d",i);fflush(stdout);  #include <gsl/gsl_multimin.h>
       linmin(p,xit,n,fret,func);  #endif
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  
         ibig=i;  #ifdef NLOPT
       }  #include <nlopt.h>
 #ifdef DEBUG  typedef struct {
       printf("%d %.12e",i,(*fret));    double (* function)(double [] );
       for (j=1;j<=n;j++) {  } myfunc_data ;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #endif
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  /* #include <libintl.h> */
       for(j=1;j<=n;j++)  /* #define _(String) gettext (String) */
         printf(" p=%.12e",p[j]);  
       printf("\n");  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
 #endif  
     }  #define GNUPLOTPROGRAM "gnuplot"
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #ifdef DEBUG  #define FILENAMELENGTH 132
       int k[2],l;  
       k[0]=1;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       k[1]=-1;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         printf(" %.12e",p[j]);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
       printf("\n");  
       for(l=0;l<=1;l++) {  #define NINTERVMAX 8
         for (j=1;j<=n;j++) {  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
         }  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #define MAXN 20000
       }  #define YEARM 12. /**< Number of months per year */
 #endif  #define AGESUP 130
   #define AGEBASE 40
   #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
       free_vector(xit,1,n);  #ifdef _WIN32
       free_vector(xits,1,n);  #define DIRSEPARATOR '\\'
       free_vector(ptt,1,n);  #define CHARSEPARATOR "\\"
       free_vector(pt,1,n);  #define ODIRSEPARATOR '/'
       return;  #else
     }  #define DIRSEPARATOR '/'
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define CHARSEPARATOR "/"
     for (j=1;j<=n;j++) {  #define ODIRSEPARATOR '\\'
       ptt[j]=2.0*p[j]-pt[j];  #endif
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  /* $Id$ */
     }  /* $State$ */
     fptt=(*func)(ptt);  
     if (fptt < fp) {  char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  char fullversion[]="$Revision$ $Date$"; 
       if (t < 0.0) {  char strstart[80];
         linmin(p,xit,n,fret,func);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
         for (j=1;j<=n;j++) {  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
           xi[j][ibig]=xi[j][n];  int nvar=0, nforce=0; /* Number of variables, number of forces */
           xi[j][n]=xit[j];  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
         }  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
 #ifdef DEBUG  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
         for(j=1;j<=n;j++)  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
           printf(" %.12e",xit[j]);  int cptcovprodnoage=0; /**< Number of covariate products without age */   
         printf("\n");  int cptcoveff=0; /* Total number of covariates to vary for printing results */
 #endif  int cptcov=0; /* Working variable */
       }  int npar=NPARMAX;
     }  int nlstate=2; /* Number of live states */
   }  int ndeath=1; /* Number of dead states */
 }  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 /**** Prevalence limit ****************/  
   int *wav; /* Number of waves for this individuual 0 is possible */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int maxwav=0; /* Maxim number of waves */
 {  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
      matrix by transitions matrix until convergence is reached */  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
   int i, ii,j,k;  int mle=1, weightopt=0;
   double min, max, maxmin, maxmax,sumnew=0.;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double **matprod2();  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double **out, cov[NCOVMAX], **pmij();  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double **newm;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double agefin, delaymax=50 ; /* Max number of years to converge */  int countcallfunc=0;  /* Count the number of calls to func */
   double jmean=1; /* Mean space between 2 waves */
   for (ii=1;ii<=nlstate+ndeath;ii++)  double **matprod2(); /* test */
     for (j=1;j<=nlstate+ndeath;j++){  double **oldm, **newm, **savm; /* Working pointers to matrices */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     }  /*FILE *fic ; */ /* Used in readdata only */
   FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    cov[1]=1.;  FILE *ficlog, *ficrespow;
    int globpr=0; /* Global variable for printing or not */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double fretone; /* Only one call to likelihood */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  long ipmx=0; /* Number of contributions */
     newm=savm;  double sw; /* Sum of weights */
     /* Covariates have to be included here again */  char filerespow[FILENAMELENGTH];
      cov[2]=agefin;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
    FILE *ficresilk;
       for (k=1; k<=cptcovn;k++) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  FILE *ficresprobmorprev;
         /*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 *fichtm, *fichtmcov; /* Html File */
       }  FILE *ficreseij;
       for (k=1; k<=cptcovage;k++)  char filerese[FILENAMELENGTH];
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  FILE *ficresstdeij;
       for (k=1; k<=cptcovprod;k++)  char fileresstde[FILENAMELENGTH];
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  FILE  *ficresvij;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
     savm=oldm;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     oldm=newm;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     maxmax=0.;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     for(j=1;j<=nlstate;j++){  char command[FILENAMELENGTH];
       min=1.;  int  outcmd=0;
       max=0.;  
       for(i=1; i<=nlstate; i++) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  char filelog[FILENAMELENGTH]; /* Log file */
         prlim[i][j]= newm[i][j]/(1-sumnew);  char filerest[FILENAMELENGTH];
         max=FMAX(max,prlim[i][j]);  char fileregp[FILENAMELENGTH];
         min=FMIN(min,prlim[i][j]);  char popfile[FILENAMELENGTH];
       }  
       maxmin=max-min;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       maxmax=FMAX(maxmax,maxmin);  
     }  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
     if(maxmax < ftolpl){  /* struct timezone tzp; */
       return prlim;  /* extern int gettimeofday(); */
     }  struct tm tml, *gmtime(), *localtime();
   }  
 }  extern time_t time();
   
 /*************** transition probabilities ***************/  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  struct tm tm;
 {  
   double s1, s2;  char strcurr[80], strfor[80];
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;  char *endptr;
   long lval;
     for(i=1; i<= nlstate; i++){  double dval;
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define NR_END 1
         /*s2 += param[i][j][nc]*cov[nc];*/  #define FREE_ARG char*
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define FTOL 1.0e-10
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  #define NRANSI 
       ps[i][j]=s2;  #define ITMAX 200 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  #define TOL 2.0e-4 
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define CGOLD 0.3819660 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define ZEPS 1.0e-10 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       }  
       ps[i][j]=s2;  #define GOLD 1.618034 
     }  #define GLIMIT 100.0 
   }  #define TINY 1.0e-20 
     /*ps[3][2]=1;*/  
   static double maxarg1,maxarg2;
   for(i=1; i<= nlstate; i++){  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
      s1=0;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     for(j=1; j<i; j++)    
       s1+=exp(ps[i][j]);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     for(j=i+1; j<=nlstate+ndeath; j++)  #define rint(a) floor(a+0.5)
       s1+=exp(ps[i][j]);  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
     ps[i][i]=1./(s1+1.);  /* #define mytinydouble 1.0e-16 */
     for(j=1; j<i; j++)  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
     for(j=i+1; j<=nlstate+ndeath; j++)  /* static double dsqrarg; */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  static double sqrarg;
   } /* end i */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  int agegomp= AGEGOMP;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  int imx; 
       ps[ii][ii]=1;  int stepm=1;
     }  /* Stepm, step in month: minimum step interpolation*/
   }  
   int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  int m,nb;
      printf("%lf ",ps[ii][jj]);  long *num;
    }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     printf("\n ");  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     }  double **pmmij, ***probs;
     printf("\n ");printf("%lf ",cov[2]);*/  double *ageexmed,*agecens;
 /*  double dateintmean=0;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/  double *weight;
     return ps;  int **s; /* Status */
 }  double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
 /**************** Product of 2 matrices ******************/                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  double  idx; 
 {  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  int *Ndum; /** Freq of modality (tricode */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   /* in, b, out are matrice of pointers which should have been initialized  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
      before: only the contents of out is modified. The function returns  double *lsurv, *lpop, *tpop;
      a pointer to pointers identical to out */  
   long i, j, k;  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   for(i=nrl; i<= nrh; i++)  double ftolhess; /**< Tolerance for computing hessian */
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /**************** split *************************/
         out[i][k] +=in[i][j]*b[j][k];  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
   return out;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 }       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
     char  *ss;                            /* pointer */
 /************* Higher Matrix Product ***************/    int   l1, l2;                         /* length counters */
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    l1 = strlen(path );                   /* length of path */
 {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      duration (i.e. until    if ( ss == NULL ) {                   /* no directory, so determine current directory */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      strcpy( name, path );               /* we got the fullname name because no directory */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
      (typically every 2 years instead of every month which is too big).        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      Model is determined by parameters x and covariates have to be      /* get current working directory */
      included manually here.      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
      */        return( GLOCK_ERROR_GETCWD );
       }
   int i, j, d, h, k;      /* got dirc from getcwd*/
   double **out, cov[NCOVMAX];      printf(" DIRC = %s \n",dirc);
   double **newm;    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
   /* Hstepm could be zero and should return the unit matrix */      l2 = strlen( ss );                  /* length of filename */
   for (i=1;i<=nlstate+ndeath;i++)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     for (j=1;j<=nlstate+ndeath;j++){      strcpy( name, ss );         /* save file name */
       oldm[i][j]=(i==j ? 1.0 : 0.0);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       po[i][j][0]=(i==j ? 1.0 : 0.0);      dirc[l1-l2] = 0;                    /* add zero */
     }      printf(" DIRC2 = %s \n",dirc);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    }
   for(h=1; h <=nhstepm; h++){    /* We add a separator at the end of dirc if not exists */
     for(d=1; d <=hstepm; d++){    l1 = strlen( dirc );                  /* length of directory */
       newm=savm;    if( dirc[l1-1] != DIRSEPARATOR ){
       /* Covariates have to be included here again */      dirc[l1] =  DIRSEPARATOR;
       cov[1]=1.;      dirc[l1+1] = 0; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      printf(" DIRC3 = %s \n",dirc);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    }
       for (k=1; k<=cptcovage;k++)    ss = strrchr( name, '.' );            /* find last / */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (ss >0){
       for (k=1; k<=cptcovprod;k++)      ss++;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
       l2= strlen(ss)+1;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      strncpy( finame, name, l1-l2);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      finame[l1-l2]= 0;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;    return( 0 );                          /* we're done */
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  
       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]);  void replace_back_to_slash(char *s, char*t)
          */  {
       }    int i;
   } /* end h */    int lg=0;
   return po;    i=0;
 }    lg=strlen(t);
     for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /*************** log-likelihood *************/      if (t[i]== '\\') s[i]='/';
 double func( double *x)    }
 {  }
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  char *trimbb(char *out, char *in)
   double **out;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   double sw; /* Sum of weights */    char *s;
   double lli; /* Individual log likelihood */    s=out;
   long ipmx;    while (*in != '\0'){
   /*extern weight */      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   /* We are differentiating ll according to initial status */        in++;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      }
   /*for(i=1;i<imx;i++)      *out++ = *in++;
     printf(" %d\n",s[4][i]);    }
   */    *out='\0';
   cov[1]=1.;    return s;
   }
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  char *cutl(char *blocc, char *alocc, char *in, char occ)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  {
     for(mi=1; mi<= wav[i]-1; mi++){    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       for (ii=1;ii<=nlstate+ndeath;ii++)       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);       gives blocc="abcdef2ghi" and alocc="j".
       for(d=0; d<dh[mi][i]; d++){       If occ is not found blocc is null and alocc is equal to in. Returns blocc
         newm=savm;    */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    char *s, *t;
         for (kk=1; kk<=cptcovage;kk++) {    t=in;s=in;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    while ((*in != occ) && (*in != '\0')){
         }      *alocc++ = *in++;
            }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    if( *in == occ){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      *(alocc)='\0';
         savm=oldm;      s=++in;
         oldm=newm;    }
           
            if (s == t) {/* occ not found */
       } /* end mult */      *(alocc-(in-s))='\0';
            in=s;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    while ( *in != '\0'){
       ipmx +=1;      *blocc++ = *in++;
       sw += weight[i];    }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */    *blocc='\0';
   } /* end of individual */    return t;
   }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  char *cutv(char *blocc, char *alocc, char *in, char occ)
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  {
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   return -l;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
 }       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
 /*********** Maximum Likelihood Estimation ***************/    char *s, *t;
     t=in;s=in;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    while (*in != '\0'){
 {      while( *in == occ){
   int i,j, iter;        *blocc++ = *in++;
   double **xi,*delti;        s=in;
   double fret;      }
   xi=matrix(1,npar,1,npar);      *blocc++ = *in++;
   for (i=1;i<=npar;i++)    }
     for (j=1;j<=npar;j++)    if (s == t) /* occ not found */
       xi[i][j]=(i==j ? 1.0 : 0.0);      *(blocc-(in-s))='\0';
   printf("Powell\n");    else
   powell(p,xi,npar,ftol,&iter,&fret,func);      *(blocc-(in-s)-1)='\0';
     in=s;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    while ( *in != '\0'){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      *alocc++ = *in++;
     }
 }  
     *alocc='\0';
 /**** Computes Hessian and covariance matrix ***/    return s;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  int nbocc(char *s, char occ)
   double **hess;  {
   int i, j,jk;    int i,j=0;
   int *indx;    int lg=20;
     i=0;
   double hessii(double p[], double delta, int theta, double delti[]);    lg=strlen(s);
   double hessij(double p[], double delti[], int i, int j);    for(i=0; i<= lg; i++) {
   void lubksb(double **a, int npar, int *indx, double b[]) ;    if  (s[i] == occ ) j++;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    }
     return j;
   hess=matrix(1,npar,1,npar);  }
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  /* void cutv(char *u,char *v, char*t, char occ) */
   for (i=1;i<=npar;i++){  /* { */
     printf("%d",i);fflush(stdout);  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     /*printf(" %f ",p[i]);*/  /*      gives u="abcdef2ghi" and v="j" *\/ */
     /*printf(" %lf ",hess[i][i]);*/  /*   int i,lg,j,p=0; */
   }  /*   i=0; */
    /*   lg=strlen(t); */
   for (i=1;i<=npar;i++) {  /*   for(j=0; j<=lg-1; j++) { */
     for (j=1;j<=npar;j++)  {  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       if (j>i) {  /*   } */
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  /*   for(j=0; j<p; j++) { */
         hess[j][i]=hess[i][j];      /*     (u[j] = t[j]); */
         /*printf(" %lf ",hess[i][j]);*/  /*   } */
       }  /*      u[p]='\0'; */
     }  
   }  /*    for(j=0; j<= lg; j++) { */
   printf("\n");  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /* } */
    
   a=matrix(1,npar,1,npar);  #ifdef _WIN32
   y=matrix(1,npar,1,npar);  char * strsep(char **pp, const char *delim)
   x=vector(1,npar);  {
   indx=ivector(1,npar);    char *p, *q;
   for (i=1;i<=npar;i++)           
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    if ((p = *pp) == NULL)
   ludcmp(a,npar,indx,&pd);      return 0;
     if ((q = strpbrk (p, delim)) != NULL)
   for (j=1;j<=npar;j++) {    {
     for (i=1;i<=npar;i++) x[i]=0;      *pp = q + 1;
     x[j]=1;      *q = '\0';
     lubksb(a,npar,indx,x);    }
     for (i=1;i<=npar;i++){    else
       matcov[i][j]=x[i];      *pp = 0;
     }    return p;
   }  }
   #endif
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {  /********************** nrerror ********************/
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  void nrerror(char error_text[])
     }  {
     printf("\n");    fprintf(stderr,"ERREUR ...\n");
   }    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   /* Recompute Inverse */  }
   for (i=1;i<=npar;i++)  /*********************** vector *******************/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  double *vector(int nl, int nh)
   ludcmp(a,npar,indx,&pd);  {
     double *v;
   /*  printf("\n#Hessian matrix recomputed#\n");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
   for (j=1;j<=npar;j++) {    return v-nl+NR_END;
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  /************************ free vector ******************/
     for (i=1;i<=npar;i++){  void free_vector(double*v, int nl, int nh)
       y[i][j]=x[i];  {
       printf("%.3e ",y[i][j]);    free((FREE_ARG)(v+nl-NR_END));
     }  }
     printf("\n");  
   }  /************************ivector *******************************/
   */  int *ivector(long nl,long nh)
   {
   free_matrix(a,1,npar,1,npar);    int *v;
   free_matrix(y,1,npar,1,npar);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   free_vector(x,1,npar);    if (!v) nrerror("allocation failure in ivector");
   free_ivector(indx,1,npar);    return v-nl+NR_END;
   free_matrix(hess,1,npar,1,npar);  }
   
   /******************free ivector **************************/
 }  void free_ivector(int *v, long nl, long nh)
   {
 /*************** hessian matrix ****************/    free((FREE_ARG)(v+nl-NR_END));
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /************************lvector *******************************/
   int l=1, lmax=20;  long *lvector(long nl,long nh)
   double k1,k2;  {
   double p2[NPARMAX+1];    long *v;
   double res;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    if (!v) nrerror("allocation failure in ivector");
   double fx;    return v-nl+NR_END;
   int k=0,kmax=10;  }
   double l1;  
   /******************free lvector **************************/
   fx=func(x);  void free_lvector(long *v, long nl, long nh)
   for (i=1;i<=npar;i++) p2[i]=x[i];  {
   for(l=0 ; l <=lmax; l++){    free((FREE_ARG)(v+nl-NR_END));
     l1=pow(10,l);  }
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  /******************* imatrix *******************************/
       delt = delta*(l1*k);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       p2[theta]=x[theta] +delt;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       k1=func(p2)-fx;  { 
       p2[theta]=x[theta]-delt;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       k2=func(p2)-fx;    int **m; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    /* allocate pointers to rows */ 
          m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()"); 
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    m += NR_END; 
 #endif    m -= nrl; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    
         k=kmax;    /* allocate rows and set pointers to them */ 
       }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         k=kmax; l=lmax*10.;    m[nrl] += NR_END; 
       }    m[nrl] -= ncl; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    
         delts=delt;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       }    
     }    /* return pointer to array of pointers to rows */ 
   }    return m; 
   delti[theta]=delts;  } 
   return res;  
    /****************** free_imatrix *************************/
 }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
 double hessij( double x[], double delti[], int thetai,int thetaj)        long nch,ncl,nrh,nrl; 
 {       /* free an int matrix allocated by imatrix() */ 
   int i;  { 
   int l=1, l1, lmax=20;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double k1,k2,k3,k4,res,fx;    free((FREE_ARG) (m+nrl-NR_END)); 
   double p2[NPARMAX+1];  } 
   int k;  
   /******************* matrix *******************************/
   fx=func(x);  double **matrix(long nrl, long nrh, long ncl, long nch)
   for (k=1; k<=2; k++) {  {
     for (i=1;i<=npar;i++) p2[i]=x[i];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     p2[thetai]=x[thetai]+delti[thetai]/k;    double **m;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      if (!m) nrerror("allocation failure 1 in matrix()");
     p2[thetai]=x[thetai]+delti[thetai]/k;    m += NR_END;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    m -= nrl;
     k2=func(p2)-fx;  
      m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     p2[thetai]=x[thetai]-delti[thetai]/k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    m[nrl] += NR_END;
     k3=func(p2)-fx;    m[nrl] -= ncl;
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    return m;
     k4=func(p2)-fx;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
 #ifdef DEBUG  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);     */
 #endif  }
   }  
   return res;  /*************************free matrix ************************/
 }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 /************** Inverse of matrix **************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 void ludcmp(double **a, int n, int *indx, double *d)    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   int i,imax,j,k;  
   double big,dum,sum,temp;  /******************* ma3x *******************************/
   double *vv;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
    {
   vv=vector(1,n);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   *d=1.0;    double ***m;
   for (i=1;i<=n;i++) {  
     big=0.0;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (j=1;j<=n;j++)    if (!m) nrerror("allocation failure 1 in matrix()");
       if ((temp=fabs(a[i][j])) > big) big=temp;    m += NR_END;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    m -= nrl;
     vv[i]=1.0/big;  
   }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (j=1;j<=n;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for (i=1;i<j;i++) {    m[nrl] += NR_END;
       sum=a[i][j];    m[nrl] -= ncl;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }  
     big=0.0;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     for (i=j;i<=n;i++) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       sum=a[i][j];    m[nrl][ncl] += NR_END;
       for (k=1;k<j;k++)    m[nrl][ncl] -= nll;
         sum -= a[i][k]*a[k][j];    for (j=ncl+1; j<=nch; j++) 
       a[i][j]=sum;      m[nrl][j]=m[nrl][j-1]+nlay;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    
         big=dum;    for (i=nrl+1; i<=nrh; i++) {
         imax=i;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       }      for (j=ncl+1; j<=nch; j++) 
     }        m[i][j]=m[i][j-1]+nlay;
     if (j != imax) {    }
       for (k=1;k<=n;k++) {    return m; 
         dum=a[imax][k];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         a[imax][k]=a[j][k];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         a[j][k]=dum;    */
       }  }
       *d = -(*d);  
       vv[imax]=vv[j];  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     indx[j]=imax;  {
     if (a[j][j] == 0.0) a[j][j]=TINY;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     if (j != n) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       dum=1.0/(a[j][j]);    free((FREE_ARG)(m+nrl-NR_END));
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  }
     }  
   }  /*************** function subdirf ***********/
   free_vector(vv,1,n);  /* Doesn't work */  char *subdirf(char fileres[])
 ;  {
 }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 void lubksb(double **a, int n, int *indx, double b[])    strcat(tmpout,"/"); /* Add to the right */
 {    strcat(tmpout,fileres);
   int i,ii=0,ip,j;    return tmpout;
   double sum;  }
    
   for (i=1;i<=n;i++) {  /*************** function subdirf2 ***********/
     ip=indx[i];  char *subdirf2(char fileres[], char *preop)
     sum=b[ip];  {
     b[ip]=b[i];    
     if (ii)    /* Caution optionfilefiname is hidden */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    strcpy(tmpout,optionfilefiname);
     else if (sum) ii=i;    strcat(tmpout,"/");
     b[i]=sum;    strcat(tmpout,preop);
   }    strcat(tmpout,fileres);
   for (i=n;i>=1;i--) {    return tmpout;
     sum=b[i];  }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
 }  {
     
 /************ Frequencies ********************/    /* Caution optionfilefiname is hidden */
 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)    strcpy(tmpout,optionfilefiname);
 {  /* Some frequencies */    strcat(tmpout,"/");
      strcat(tmpout,preop);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    strcat(tmpout,preop2);
   double ***freq; /* Frequencies */    strcat(tmpout,fileres);
   double *pp;    return tmpout;
   double pos, k2, dateintsum=0,k2cpt=0;  }
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  char *asc_diff_time(long time_sec, char ascdiff[])
    {
   pp=vector(1,nlstate);    long sec_left, days, hours, minutes;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    days = (time_sec) / (60*60*24);
   strcpy(fileresp,"p");    sec_left = (time_sec) % (60*60*24);
   strcat(fileresp,fileres);    hours = (sec_left) / (60*60) ;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    sec_left = (sec_left) %(60*60);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    minutes = (sec_left) /60;
     exit(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);  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    return ascdiff;
   j1=0;  }
   
   j=cptcoveff;  /***************** f1dim *************************/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  extern int ncom; 
   extern double *pcom,*xicom;
   for(k1=1; k1<=j;k1++){  extern double (*nrfunc)(double []); 
    for(i1=1; i1<=ncodemax[k1];i1++){   
        j1++;  double f1dim(double x) 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  { 
          scanf("%d", i);*/    int j; 
         for (i=-1; i<=nlstate+ndeath; i++)      double f;
          for (jk=-1; jk<=nlstate+ndeath; jk++)      double *xt; 
            for(m=agemin; m <= agemax+3; m++)   
              freq[i][jk][m]=0;    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         dateintsum=0;    f=(*nrfunc)(xt); 
         k2cpt=0;    free_vector(xt,1,ncom); 
        for (i=1; i<=imx; i++) {    return f; 
          bool=1;  } 
          if  (cptcovn>0) {  
            for (z1=1; z1<=cptcoveff; z1++)  /*****************brent *************************/
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
                bool=0;  { 
          }    int iter; 
          if (bool==1) {    double a,b,d,etemp;
            for(m=firstpass; m<=lastpass; m++){    double fu=0,fv,fw,fx;
              k2=anint[m][i]+(mint[m][i]/12.);    double ftemp=0.;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
                if(agev[m][i]==0) agev[m][i]=agemax+1;    double e=0.0; 
                if(agev[m][i]==1) agev[m][i]=agemax+2;   
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    a=(ax < cx ? ax : cx); 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    b=(ax > cx ? ax : cx); 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    x=w=v=bx; 
                  dateintsum=dateintsum+k2;    fw=fv=fx=(*f)(x); 
                  k2cpt++;    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(ficlog,".");fflush(ficlog);
        }  #ifdef DEBUGBRENT
              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, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         if  (cptcovn>0) {  #endif
          fprintf(ficresp, "\n#********** Variable ");      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        *xmin=x; 
        fprintf(ficresp, "**********\n#");        return fx; 
         }      } 
        for(i=1; i<=nlstate;i++)      ftemp=fu;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      if (fabs(e) > tol1) { 
        fprintf(ficresp, "\n");        r=(x-w)*(fx-fv); 
                q=(x-v)*(fx-fw); 
   for(i=(int)agemin; i <= (int)agemax+3; i++){        p=(x-v)*q-(x-w)*r; 
     if(i==(int)agemax+3)        q=2.0*(q-r); 
       printf("Total");        if (q > 0.0) p = -p; 
     else        q=fabs(q); 
       printf("Age %d", i);        etemp=e; 
     for(jk=1; jk <=nlstate ; jk++){        e=d; 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         pp[jk] += freq[jk][m][i];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }        else { 
     for(jk=1; jk <=nlstate ; jk++){          d=p/q; 
       for(m=-1, pos=0; m <=0 ; m++)          u=x+d; 
         pos += freq[jk][m][i];          if (u-a < tol2 || b-u < tol2) 
       if(pp[jk]>=1.e-10)            d=SIGN(tol1,xm-x); 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        } 
       else      } else { 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
      for(jk=1; jk <=nlstate ; jk++){      fu=(*f)(u); 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      if (fu <= fx) { 
         pp[jk] += freq[jk][m][i];        if (u >= x) a=x; else b=x; 
      }        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
     for(jk=1,pos=0; jk <=nlstate ; jk++)          } else { 
       pos += pp[jk];            if (u < x) a=u; else b=u; 
     for(jk=1; jk <=nlstate ; jk++){            if (fu <= fw || w == x) { 
       if(pos>=1.e-5)              v=w; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              w=u; 
       else              fv=fw; 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              fw=fu; 
       if( i <= (int) agemax){            } else if (fu <= fv || v == x || v == w) { 
         if(pos>=1.e-5){              v=u; 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);              fv=fu; 
           probs[i][jk][j1]= pp[jk]/pos;            } 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          } 
         }    } 
       else    nrerror("Too many iterations in brent"); 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    *xmin=x; 
       }    return fx; 
     }  } 
     for(jk=-1; jk <=nlstate+ndeath; jk++)  
       for(m=-1; m <=nlstate+ndeath; m++)  /****************** mnbrak ***********************/
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       fprintf(ficresp,"\n");              double (*func)(double)) 
     printf("\n");  { 
     }    double ulim,u,r,q, dum;
     }    double fu; 
  }   
   dateintmean=dateintsum/k2cpt;    *fa=(*func)(*ax); 
      *fb=(*func)(*bx); 
   fclose(ficresp);    if (*fb > *fa) { 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      SHFT(dum,*ax,*bx,dum) 
   free_vector(pp,1,nlstate);        SHFT(dum,*fb,*fa,dum) 
         } 
   /* End of Freq */    *cx=(*bx)+GOLD*(*bx-*ax); 
 }    *fc=(*func)(*cx); 
     while (*fb > *fc) { /* Declining fa, fb, fc */
 /************ Prevalence ********************/      r=(*bx-*ax)*(*fb-*fc); 
 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)      q=(*bx-*cx)*(*fb-*fa); 
 {  /* Some frequencies */      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
          (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
   double ***freq; /* Frequencies */      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
   double *pp;        fu=(*func)(u); 
   double pos, k2;  #ifdef DEBUG
         /* f(x)=A(x-u)**2+f(u) */
   pp=vector(1,nlstate);        double A, fparabu; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
          fparabu= *fa - A*(*ax-u)*(*ax-u);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        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);
   j1=0;        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 
   j=cptcoveff;      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        fu=(*func)(u); 
          if (fu < *fc) { 
  for(k1=1; k1<=j;k1++){          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for(i1=1; i1<=ncodemax[k1];i1++){            SHFT(*fb,*fc,fu,(*func)(u)) 
       j1++;            } 
        } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
       for (i=-1; i<=nlstate+ndeath; i++)          u=ulim; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          fu=(*func)(u); 
           for(m=agemin; m <= agemax+3; m++)      } else { 
             freq[i][jk][m]=0;        u=(*cx)+GOLD*(*cx-*bx); 
              fu=(*func)(u); 
       for (i=1; i<=imx; i++) {      } 
         bool=1;      SHFT(*ax,*bx,*cx,u) 
         if  (cptcovn>0) {        SHFT(*fa,*fb,*fc,fu) 
           for (z1=1; z1<=cptcoveff; z1++)        } 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  } 
               bool=0;  
         }  /*************** linmin ************************/
         if (bool==1) {  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
           for(m=firstpass; m<=lastpass; m++){  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
             k2=anint[m][i]+(mint[m][i]/12.);  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  the value of func at the returned location p . This is actually all accomplished by calling the
               if(agev[m][i]==0) agev[m][i]=agemax+1;  routines mnbrak and brent .*/
               if(agev[m][i]==1) agev[m][i]=agemax+2;  int ncom; 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  double *pcom,*xicom;
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  double (*nrfunc)(double []); 
             }   
           }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         }  { 
       }    double brent(double ax, double bx, double cx, 
         for(i=(int)agemin; i <= (int)agemax+3; i++){                 double (*f)(double), double tol, double *xmin); 
           for(jk=1; jk <=nlstate ; jk++){    double f1dim(double x); 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
               pp[jk] += freq[jk][m][i];                double *fc, double (*func)(double)); 
           }    int j; 
           for(jk=1; jk <=nlstate ; jk++){    double xx,xmin,bx,ax; 
             for(m=-1, pos=0; m <=0 ; m++)    double fx,fb,fa;
             pos += freq[jk][m][i];   
         }    ncom=n; 
            pcom=vector(1,n); 
          for(jk=1; jk <=nlstate ; jk++){    xicom=vector(1,n); 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    nrfunc=func; 
              pp[jk] += freq[jk][m][i];    for (j=1;j<=n;j++) { 
          }      pcom[j]=p[j]; 
                xicom[j]=xi[j]; 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    } 
     ax=0.0; 
          for(jk=1; jk <=nlstate ; jk++){              xx=1.0; 
            if( i <= (int) agemax){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
              if(pos>=1.e-5){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
                probs[i][jk][j1]= pp[jk]/pos;  #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_vector(xicom,1,n); 
      free_vector(pcom,1,n); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  } 
   free_vector(pp,1,nlstate);  
    
 }  /* End of Freq */  /*************** powell ************************/
   /*
 /************* Waves Concatenation ***************/  Minimization of a function func of n variables. Input consists of an initial starting point
   p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
 {  such that failure to decrease by more than this amount on one iteration signals doneness. On
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
      Death is a valid wave (if date is known).  function value at p , and iter is the number of iterations taken. The routine linmin is used.
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i   */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
      and mw[mi+1][i]. dh depends on stepm.              double (*func)(double [])) 
      */  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   int i, mi, m;                double (*func)(double [])); 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    int i,ibig,j; 
      double sum=0., jmean=0.;*/    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
   int j, k=0,jk, ju, jl;    double *xits;
   double sum=0.;    int niterf, itmp;
   jmin=1e+5;  
   jmax=-1;    pt=vector(1,n); 
   jmean=0.;    ptt=vector(1,n); 
   for(i=1; i<=imx; i++){    xit=vector(1,n); 
     mi=0;    xits=vector(1,n); 
     m=firstpass;    *fret=(*func)(p); 
     while(s[m][i] <= nlstate){    for (j=1;j<=n;j++) pt[j]=p[j]; 
       if(s[m][i]>=1)      rcurr_time = time(NULL);  
         mw[++mi][i]=m;    for (*iter=1;;++(*iter)) { 
       if(m >=lastpass)      fp=(*fret); 
         break;      ibig=0; 
       else      del=0.0; 
         m++;      rlast_time=rcurr_time;
     }/* end while */      /* (void) gettimeofday(&curr_time,&tzp); */
     if (s[m][i] > nlstate){      rcurr_time = time(NULL);  
       mi++;     /* Death is another wave */      curr_time = *localtime(&rcurr_time);
       /* if(mi==0)  never been interviewed correctly before death */      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
          /* Only death is a correct wave */      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
       mw[mi][i]=m;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
     }     for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
     wav[i]=mi;        fprintf(ficlog," %d %.12lf",i, p[i]);
     if(mi==0)        fprintf(ficrespow," %.12lf", p[i]);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      }
   }      printf("\n");
       fprintf(ficlog,"\n");
   for(i=1; i<=imx; i++){      fprintf(ficrespow,"\n");fflush(ficrespow);
     for(mi=1; mi<wav[i];mi++){      if(*iter <=3){
       if (stepm <=0)        tml = *localtime(&rcurr_time);
         dh[mi][i]=1;        strcpy(strcurr,asctime(&tml));
       else{        rforecast_time=rcurr_time; 
         if (s[mw[mi+1][i]][i] > nlstate) {        itmp = strlen(strcurr);
           if (agedc[i] < 2*AGESUP) {        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          strcurr[itmp-1]='\0';
           if(j==0) j=1;  /* Survives at least one month after exam */        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           k=k+1;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           if (j >= jmax) jmax=j;        for(niterf=10;niterf<=30;niterf+=10){
           if (j <= jmin) jmin=j;          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
           sum=sum+j;          forecast_time = *localtime(&rforecast_time);
           /* if (j<10) printf("j=%d num=%d ",j,i); */          strcpy(strfor,asctime(&forecast_time));
           }          itmp = strlen(strfor);
         }          if(strfor[itmp-1]=='\n')
         else{          strfor[itmp-1]='\0';
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          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);
           k=k+1;          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);
           if (j >= jmax) jmax=j;        }
           else if (j <= jmin)jmin=j;      }
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      for (i=1;i<=n;i++) { 
           sum=sum+j;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         }        fptt=(*fret); 
         jk= j/stepm;  #ifdef DEBUG
         jl= j -jk*stepm;            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
         ju= j -(jk+1)*stepm;            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
         if(jl <= -ju)  #endif
           dh[mi][i]=jk;        printf("%d",i);fflush(stdout);
         else        fprintf(ficlog,"%d",i);fflush(ficlog);
           dh[mi][i]=jk+1;        linmin(p,xit,n,fret,func); 
         if(dh[mi][i]==0)        if (fabs(fptt-(*fret)) > del) { 
           dh[mi][i]=1; /* At least one step */          del=fabs(fptt-(*fret)); 
       }          ibig=i; 
     }        } 
   }  #ifdef DEBUG
   jmean=sum/k;        printf("%d %.12e",i,(*fret));
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        fprintf(ficlog,"%d %.12e",i,(*fret));
  }        for (j=1;j<=n;j++) {
 /*********** Tricode ****************************/          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 void tricode(int *Tvar, int **nbcode, int imx)          printf(" x(%d)=%.12e",j,xit[j]);
 {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   int Ndum[20],ij=1, k, j, i;        }
   int cptcode=0;        for(j=1;j<=n;j++) {
   cptcoveff=0;          printf(" p(%d)=%.12e",j,p[j]);
            fprintf(ficlog," p(%d)=%.12e",j,p[j]);
   for (k=0; k<19; k++) Ndum[k]=0;        }
   for (k=1; k<=7; k++) ncodemax[k]=0;        printf("\n");
         fprintf(ficlog,"\n");
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  #endif
     for (i=1; i<=imx; i++) {      } /* end i */
       ij=(int)(covar[Tvar[j]][i]);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       Ndum[ij]++;  #ifdef DEBUG
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        int k[2],l;
       if (ij > cptcode) cptcode=ij;        k[0]=1;
     }        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
     for (i=0; i<=cptcode; i++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
       if(Ndum[i]!=0) ncodemax[j]++;        for (j=1;j<=n;j++) {
     }          printf(" %.12e",p[j]);
     ij=1;          fprintf(ficlog," %.12e",p[j]);
         }
         printf("\n");
     for (i=1; i<=ncodemax[j]; i++) {        fprintf(ficlog,"\n");
       for (k=0; k<=19; k++) {        for(l=0;l<=1;l++) {
         if (Ndum[k] != 0) {          for (j=1;j<=n;j++) {
           nbcode[Tvar[j]][ij]=k;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
           ij++;            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]);
         if (ij > ncodemax[j]) break;          }
       }            printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   }          }
   #endif
  for (k=0; k<19; k++) Ndum[k]=0;  
   
  for (i=1; i<=ncovmodel-2; i++) {        free_vector(xit,1,n); 
       ij=Tvar[i];        free_vector(xits,1,n); 
       Ndum[ij]++;        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
         return; 
  ij=1;      } 
  for (i=1; i<=10; i++) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
    if((Ndum[i]!=0) && (i<=ncov)){      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
      Tvaraff[ij]=i;        ptt[j]=2.0*p[j]-pt[j]; 
      ij++;        xit[j]=p[j]-pt[j]; 
    }        pt[j]=p[j]; 
  }      } 
        fptt=(*func)(ptt); 
     cptcoveff=ij-1;      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) */
         /* From x1 (P0) distance of x2 is at h and x3 is 2h */
 /*********** Health Expectancies ****************/        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
         /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
 {        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
   /* Health expectancies */        /* Thus we compare delta(2h) with observed f1-f3 */
   int i, j, nhstepm, hstepm, h;        /* or best gain on one ancient line 'del' with total  */
   double age, agelim,hf;        /* gain f1-f2 = f1 - f2 - 'del' with del  */
   double ***p3mat;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
    
   fprintf(ficreseij,"# Health expectancies\n");        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
   fprintf(ficreseij,"# Age");        t= t- del*SQR(fp-fptt);
   for(i=1; i<=nlstate;i++)        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
     for(j=1; j<=nlstate;j++)        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);
       fprintf(ficreseij," %1d-%1d",i,j);  #ifdef DEBUG
   fprintf(ficreseij,"\n");        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   hstepm=1*YEARM; /*  Every j years of age (in month) */        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         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);
   agelim=AGESUP;        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);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #endif
     /* nhstepm age range expressed in number of stepm */        if (t < 0.0) { /* Then we use it for last direction */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
     /* Typically if 20 years = 20*12/6=40 stepm */          for (j=1;j<=n;j++) { 
     if (stepm >= YEARM) hstepm=1;            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
   #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(i=1; i<=nlstate;i++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for(j=1; j<=nlstate;j++)          for(j=1;j<=n;j++){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            printf(" %.12e",xit[j]);
           eij[i][j][(int)age] +=p3mat[i][j][h];            fprintf(ficlog," %.12e",xit[j]);
         }          }
              printf("\n");
     hf=1;          fprintf(ficlog,"\n");
     if (stepm >= YEARM) hf=stepm/YEARM;  #endif
     fprintf(ficreseij,"%.0f",age );        } /* end of t negative */
     for(i=1; i<=nlstate;i++)      } /* end if (fptt < fp)  */
       for(j=1; j<=nlstate;j++){    } 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  } 
       }  
     fprintf(ficreseij,"\n");  /**** Prevalence limit (stable or period prevalence)  ****************/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 }  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 /************ Variance ******************/       matrix by transitions matrix until convergence is reached */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    
 {    int i, ii,j,k;
   /* Variance of health expectancies */    double min, max, maxmin, maxmax,sumnew=0.;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /* double **matprod2(); */ /* test */
   double **newm;    double **out, cov[NCOVMAX+1], **pmij();
   double **dnewm,**doldm;    double **newm;
   int i, j, nhstepm, hstepm, h;    double agefin, delaymax=50 ; /* Max number of years to converge */
   int k, cptcode;    
   double *xp;    for (ii=1;ii<=nlstate+ndeath;ii++)
   double **gp, **gm;      for (j=1;j<=nlstate+ndeath;j++){
   double ***gradg, ***trgradg;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***p3mat;      }
   double age,agelim;    
   int theta;    cov[1]=1.;
     
    fprintf(ficresvij,"# Covariances of life expectancies\n");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   fprintf(ficresvij,"# Age");    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for(i=1; i<=nlstate;i++)      newm=savm;
     for(j=1; j<=nlstate;j++)      /* Covariates have to be included here again */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      cov[2]=agefin;
   fprintf(ficresvij,"\n");      
       for (k=1; k<=cptcovn;k++) {
   xp=vector(1,npar);        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   dnewm=matrix(1,nlstate,1,npar);        /*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]]);*/
   doldm=matrix(1,nlstate,1,nlstate);      }
        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   hstepm=1*YEARM; /* Every year of age */      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   agelim = AGESUP;      
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     if (stepm >= YEARM) hstepm=1;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
     gp=matrix(0,nhstepm,1,nlstate);      
     gm=matrix(0,nhstepm,1,nlstate);      savm=oldm;
       oldm=newm;
     for(theta=1; theta <=npar; theta++){      maxmax=0.;
       for(i=1; i<=npar; i++){ /* Computes gradient */      for(j=1;j<=nlstate;j++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        min=1.;
       }        max=0.;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for(i=1; i<=nlstate; i++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       if (popbased==1) {          prlim[i][j]= newm[i][j]/(1-sumnew);
         for(i=1; i<=nlstate;i++)          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           prlim[i][i]=probs[(int)age][i][ij];          max=FMAX(max,prlim[i][j]);
       }          min=FMIN(min,prlim[i][j]);
          }
       for(j=1; j<= nlstate; j++){        maxmin=max-min;
         for(h=0; h<=nhstepm; h++){        maxmax=FMAX(maxmax,maxmin);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      } /* j loop */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      if(maxmax < ftolpl){
         }        return prlim;
       }      }
        } /* age loop */
       for(i=1; i<=npar; i++) /* Computes gradient */    return prlim; /* should not reach here */
         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);  /*************** transition probabilities ***************/ 
    
       if (popbased==1) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         for(i=1; i<=nlstate;i++)  {
           prlim[i][i]=probs[(int)age][i][ij];    /* According to parameters values stored in x and the covariate's values stored in cov,
       }       computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
       for(j=1; j<= nlstate; j++){       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         for(h=0; h<=nhstepm; h++){       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)       ncth covariate in the global vector x is given by the formula:
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
         }       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       }       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        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]
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    */
         }    double s1, lnpijopii;
     } /* End theta */    /*double t34;*/
     int i,j, nc, ii, jj;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
       for(i=1; i<= nlstate; i++){
     for(h=0; h<=nhstepm; h++)        for(j=1; j<i;j++){
       for(j=1; j<=nlstate;j++)          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         for(theta=1; theta <=npar; theta++)            /*lnpijopii += param[i][j][nc]*cov[nc];*/
           trgradg[h][j][theta]=gradg[h][theta][j];            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     for(i=1;i<=nlstate;i++)          }
       for(j=1;j<=nlstate;j++)          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         vareij[i][j][(int)age] =0.;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     for(h=0;h<=nhstepm;h++){        }
       for(k=0;k<=nhstepm;k++){        for(j=i+1; j<=nlstate+ndeath;j++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            /*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] += doldm[i][j];          }
       }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     }        }
     h=1;      }
     if (stepm >= YEARM) h=stepm/YEARM;      
     fprintf(ficresvij,"%.0f ",age );      for(i=1; i<= nlstate; i++){
     for(i=1; i<=nlstate;i++)        s1=0;
       for(j=1; j<=nlstate;j++){        for(j=1; j<i; j++){
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          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); */
     fprintf(ficresvij,"\n");        }
     free_matrix(gp,0,nhstepm,1,nlstate);        for(j=i+1; j<=nlstate+ndeath; j++){
     free_matrix(gm,0,nhstepm,1,nlstate);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   } /* End age */        ps[i][i]=1./(s1+1.);
          /* Computing other pijs */
   free_vector(xp,1,npar);        for(j=1; j<i; j++)
   free_matrix(doldm,1,nlstate,1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   free_matrix(dnewm,1,nlstate,1,nlstate);        for(j=i+1; j<=nlstate+ndeath; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
 }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
 /************ 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=nlstate+1; ii<= nlstate+ndeath; ii++){
 {        for(jj=1; jj<= nlstate+ndeath; jj++){
   /* Variance of prevalence limit */          ps[ii][jj]=0;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          ps[ii][ii]=1;
   double **newm;        }
   double **dnewm,**doldm;      }
   int i, j, nhstepm, hstepm;      
   int k, cptcode;      
   double *xp;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   double *gp, *gm;      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   double **gradg, **trgradg;      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   double age,agelim;      /*   } */
   int theta;      /*   printf("\n "); */
          /* } */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      /* printf("\n ");printf("%lf ",cov[2]);*/
   fprintf(ficresvpl,"# Age");      /*
   for(i=1; i<=nlstate;i++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       fprintf(ficresvpl," %1d-%1d",i,i);        goto end;*/
   fprintf(ficresvpl,"\n");      return ps;
   }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  /**************** Product of 2 matrices ******************/
   doldm=matrix(1,nlstate,1,nlstate);  
    double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   hstepm=1*YEARM; /* Every year of age */  {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   agelim = AGESUP;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* in, b, out are matrice of pointers which should have been initialized 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       before: only the contents of out is modified. The function returns
     if (stepm >= YEARM) hstepm=1;       a pointer to pointers identical to out */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int i, j, k;
     gradg=matrix(1,npar,1,nlstate);    for(i=nrl; i<= nrh; i++)
     gp=vector(1,nlstate);      for(k=ncolol; k<=ncoloh; k++){
     gm=vector(1,nlstate);        out[i][k]=0.;
         for(j=ncl; j<=nch; j++)
     for(theta=1; theta <=npar; theta++){          out[i][k] +=in[i][j]*b[j][k];
       for(i=1; i<=npar; i++){ /* Computes gradient */      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    return out;
       }  }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];  /************* Higher Matrix Product ***************/
      
       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);  {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* Computes the transition matrix starting at age 'age' over 
       for(i=1;i<=nlstate;i++)       'nhstepm*hstepm*stepm' months (i.e. until
         gm[i] = prlim[i][i];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
       for(i=1;i<=nlstate;i++)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       (typically every 2 years instead of every month which is too big 
     } /* End theta */       for the memory).
        Model is determined by parameters x and covariates have to be 
     trgradg =matrix(1,nlstate,1,npar);       included manually here. 
   
     for(j=1; j<=nlstate;j++)       */
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];    int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
     for(i=1;i<=nlstate;i++)    double **newm;
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    /* Hstepm could be zero and should return the unit matrix */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    for (i=1;i<=nlstate+ndeath;i++)
     for(i=1;i<=nlstate;i++)      for (j=1;j<=nlstate+ndeath;j++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
     fprintf(ficresvpl,"%.0f ",age );      }
     for(i=1; i<=nlstate;i++)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    for(h=1; h <=nhstepm; h++){
     fprintf(ficresvpl,"\n");      for(d=1; d <=hstepm; d++){
     free_vector(gp,1,nlstate);        newm=savm;
     free_vector(gm,1,nlstate);        /* Covariates have to be included here again */
     free_matrix(gradg,1,npar,1,nlstate);        cov[1]=1.;
     free_matrix(trgradg,1,nlstate,1,npar);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   } /* End age */        for (k=1; k<=cptcovn;k++) 
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   free_vector(xp,1,npar);        for (k=1; k<=cptcovage;k++)
   free_matrix(doldm,1,nlstate,1,npar);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   free_matrix(dnewm,1,nlstate,1,nlstate);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 }  
   
 /************ Variance of one-step probabilities  ******************/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   int i, j;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   int k=0, cptcode;        savm=oldm;
   double **dnewm,**doldm;        oldm=newm;
   double *xp;      }
   double *gp, *gm;      for(i=1; i<=nlstate+ndeath; i++)
   double **gradg, **trgradg;        for(j=1;j<=nlstate+ndeath;j++) {
   double age,agelim, cov[NCOVMAX];          po[i][j][h]=newm[i][j];
   int theta;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   char fileresprob[FILENAMELENGTH];        }
       /*printf("h=%d ",h);*/
   strcpy(fileresprob,"prob");    } /* end h */
   strcat(fileresprob,fileres);  /*     printf("\n H=%d \n",h); */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    return po;
     printf("Problem with resultfile: %s\n", fileresprob);  }
   }  
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  #ifdef NLOPT
      double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     double fret;
   xp=vector(1,npar);    double *xt;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int j;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    myfunc_data *d2 = (myfunc_data *) pd;
    /* xt = (p1-1); */
   cov[1]=1;    xt=vector(1,n); 
   for (age=bage; age<=fage; age ++){    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
     cov[2]=age;  
     gradg=matrix(1,npar,1,9);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     trgradg=matrix(1,9,1,npar);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    printf("Function = %.12lf ",fret);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
        printf("\n");
     for(theta=1; theta <=npar; theta++){   free_vector(xt,1,n);
       for(i=1; i<=npar; i++)    return fret;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  }
        #endif
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
      /*************** log-likelihood *************/
       k=0;  double func( double *x)
       for(i=1; i<= (nlstate+ndeath); i++){  {
         for(j=1; j<=(nlstate+ndeath);j++){    int i, ii, j, k, mi, d, kk;
            k=k+1;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           gp[k]=pmmij[i][j];    double **out;
         }    double sw; /* Sum of weights */
       }    double lli; /* Individual log likelihood */
     int s1, s2;
       for(i=1; i<=npar; i++)    double bbh, survp;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    long ipmx;
        /*extern weight */
     /* We are differentiating ll according to initial status */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       k=0;    /*for(i=1;i<imx;i++) 
       for(i=1; i<=(nlstate+ndeath); i++){      printf(" %d\n",s[4][i]);
         for(j=1; j<=(nlstate+ndeath);j++){    */
           k=k+1;  
           gm[k]=pmmij[i][j];    ++countcallfunc;
         }  
       }    cov[1]=1.;
        
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
     }    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        /* Computes the values of the ncovmodel covariates of the model
       for(theta=1; theta <=npar; theta++)           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       trgradg[j][theta]=gradg[theta][j];           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
             to be observed in j being in i according to the model.
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);         */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
           cov[2+k]=covar[Tvar[k]][i];
      pmij(pmmij,cov,ncovmodel,x,nlstate);        }
         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
      k=0;           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
      for(i=1; i<=(nlstate+ndeath); i++){           has been calculated etc */
        for(j=1; j<=(nlstate+ndeath);j++){        for(mi=1; mi<= wav[i]-1; mi++){
          k=k+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
          gm[k]=pmmij[i][j];            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);
                  }
      /*printf("\n%d ",(int)age);          for(d=0; d<dh[mi][i]; d++){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            newm=savm;
                    cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              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,
   fprintf(ficresprob,"\n%d ",(int)age);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            oldm=newm;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          } /* end mult */
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],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.
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));           * (in months) between two waves is not a multiple of stepm, we rounded to 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);           * the nearest (and in case of equal distance, to the lowest) interval but now
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
  free_vector(xp,1,npar);           * probability in order to take into account the bias as a fraction of the way
 fclose(ficresprob);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
 /******************* Printing html file ***********/           */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){          s1=s[mw[mi][i]][i];
   int jj1, k1, i1, cpt;          s2=s[mw[mi+1][i]][i];
   FILE *fichtm;          bbh=(double)bh[mi][i]/(double)stepm; 
   /*char optionfilehtm[FILENAMELENGTH];*/          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   strcpy(optionfilehtm,optionfile);           */
   strcat(optionfilehtm,".htm");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          if( s2 > nlstate){ 
     printf("Problem with %s \n",optionfilehtm), exit(0);            /* i.e. if s2 is a death state and if the date of death is known 
   }               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">               which is also equal to probability to die before dh 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>               minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
 Total number of observations=%d <br>          as if date of death was unknown. Death was treated as any other
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          health state: the date of the interview describes the actual state
 <hr  size=\"2\" color=\"#EC5E5E\">          and not the date of a change in health state. The former idea was
 <li>Outputs files<br><br>\n          to consider that at each interview the state was recorded
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          (healthy, disable or death) and IMaCh was corrected; but when we
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          introduced the exact date of death then we should have modified
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          the contribution of an exact death to the likelihood. This new
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>          contribution is smaller and very dependent of the step unit
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          stepm. It is no more the probability to die between last interview
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          and month of death but the probability to survive from last
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          interview up to one month before death multiplied by the
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          probability to die within a month. Thanks to Chris
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>          Jackson for correcting this bug.  Former versions increased
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>          mortality artificially. The bad side is that we add another loop
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>          which slows down the processing. The difference can be up to 10%
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          lower mortality.
              */
 fprintf(fichtm," <li>Graphs</li><p>");            lli=log(out[s1][s2] - savm[s1][s2]);
   
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
  jj1=0;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
  for(k1=1; k1<=m;k1++){            /*survp += out[s1][j]; */
    for(i1=1; i1<=ncodemax[k1];i1++){            lli= log(survp);
        jj1++;          }
        if (cptcovn > 0) {          
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          else if  (s2==-4) { 
          for (cpt=1; cpt<=cptcoveff;cpt++)            for (j=3,survp=0. ; j<=nlstate; j++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            lli= log(survp); 
        }          } 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              else if  (s2==-5) { 
        for(cpt=1; cpt<nlstate;cpt++){            for (j=1,survp=0. ; j<=2; j++)  
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            lli= log(survp); 
        }          } 
     for(cpt=1; cpt<=nlstate;cpt++) {          
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          else{
 interval) in state (%d): v%s%d%d.gif <br>            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              /*  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(cpt=1; cpt<=nlstate;cpt++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          /*if(lli ==000.0)*/
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
      }          ipmx +=1;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          sw += weight[i];
 health expectancies in states (1) and (2): e%s%d.gif<br>          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        } /* end of wave */
 fprintf(fichtm,"\n</body>");      } /* end of individual */
    }    }  else if(mle==2){
    }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 fclose(fichtm);        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++)
 /******************* Gnuplot file **************/            for (j=1;j<=nlstate+ndeath;j++){
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            }
           for(d=0; d<=dh[mi][i]; d++){
   strcpy(optionfilegnuplot,optionfilefiname);            newm=savm;
   strcat(optionfilegnuplot,".plt");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            for (kk=1; kk<=cptcovage;kk++) {
     printf("Problem with file %s",optionfilegnuplot);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #ifdef windows                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficgp,"cd \"%s\" \n",pathc);            savm=oldm;
 #endif            oldm=newm;
 m=pow(2,cptcoveff);          } /* end mult */
          
  /* 1eme*/          s1=s[mw[mi][i]][i];
   for (cpt=1; cpt<= nlstate ; cpt ++) {          s2=s[mw[mi+1][i]][i];
    for (k1=1; k1<= m ; k1 ++) {          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 #ifdef windows          ipmx +=1;
     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);          sw += weight[i];
 #endif          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 #ifdef unix        } /* end of wave */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      } /* end of individual */
 #endif    }  else if(mle==3){  /* exponential inter-extrapolation */
       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];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(mi=1; mi<= wav[i]-1; mi++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (ii=1;ii<=nlstate+ndeath;ii++)
 }            for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1; i<= nlstate ; i ++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(d=0; d<dh[mi][i]; d++){
 }            newm=savm;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      for (i=1; i<= nlstate ; i ++) {            for (kk=1; kk<=cptcovage;kk++) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #ifdef unix            savm=oldm;
 fprintf(ficgp,"\nset ter gif small size 400,300");            oldm=newm;
 #endif          } /* end mult */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        
    }          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   /*2 eme*/          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   for (k1=1; k1<= m ; k1 ++) {          ipmx +=1;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          sw += weight[i];
              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1; i<= nlstate+1 ; i ++) {        } /* end of wave */
       k=2*i;      } /* end of individual */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (j=1; j<= nlstate+1 ; j ++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(mi=1; mi<= wav[i]-1; mi++){
 }            for (ii=1;ii<=nlstate+ndeath;ii++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            for (j=1;j<=nlstate+ndeath;j++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*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;
       fprintf(ficgp,"\" t\"\" w l 0,");            for (kk=1; kk<=cptcovage;kk++) {
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for (j=1; j<= nlstate+1 ; j ++) {            }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          
   else fprintf(ficgp," \%%*lf (\%%*lf)");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            savm=oldm;
       else fprintf(ficgp,"\" t\"\" w l 0,");            oldm=newm;
     }          } /* end mult */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        
   }          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   /*3eme*/          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
   for (k1=1; k1<= m ; k1 ++) {          }else{
     for (cpt=1; cpt<= nlstate ; cpt ++) {            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       k=2+nlstate*(cpt-1);          }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          ipmx +=1;
       for (i=1; i< nlstate ; i ++) {          sw += weight[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);          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]); */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        } /* end of wave */
     }      } /* end of individual */
     }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* CV preval stat */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (k1=1; k1<= m ; k1 ++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (cpt=1; cpt<nlstate ; cpt ++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       k=3;            for (j=1;j<=nlstate+ndeath;j++){
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (i=1; i< nlstate ; i ++)            }
         fprintf(ficgp,"+$%d",k+i+1);          for(d=0; d<dh[mi][i]; d++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            newm=savm;
                  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       l=3+(nlstate+ndeath)*cpt;            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for (i=1; i< nlstate ; i ++) {            }
         l=3+(nlstate+ndeath)*cpt;          
         fprintf(ficgp,"+$%d",l+i+1);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              savm=oldm;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            oldm=newm;
     }          } /* end mult */
   }          
            s1=s[mw[mi][i]][i];
   /* proba elementaires */          s2=s[mw[mi+1][i]][i];
    for(i=1,jk=1; i <=nlstate; i++){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(k=1; k <=(nlstate+ndeath); k++){          ipmx +=1;
       if (k != i) {          sw += weight[i];
         for(j=1; j <=ncovmodel; j++){          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]);*/
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        } /* end of wave */
           jk++;      } /* end of individual */
           fprintf(ficgp,"\n");    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    return -l;
   }
     for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);  /*************** log-likelihood *************/
    i=1;  double funcone( double *x)
    for(k2=1; k2<=nlstate; k2++) {  {
      k3=i;    /* Same as likeli but slower because of a lot of printf and if */
      for(k=1; k<=(nlstate+ndeath); k++) {    int i, ii, j, k, mi, d, kk;
        if (k != k2){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    double **out;
 ij=1;    double lli; /* Individual log likelihood */
         for(j=3; j <=ncovmodel; j++) {    double llt;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    int s1, s2;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double bbh, survp;
             ij++;    /*extern weight */
           }    /* We are differentiating ll according to initial status */
           else    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /*for(i=1;i<imx;i++) 
         }      printf(" %d\n",s[4][i]);
           fprintf(ficgp,")/(1");    */
            cov[1]=1.;
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    for(k=1; k<=nlstate; k++) ll[k]=0.;
 ij=1;  
           for(j=3; j <=ncovmodel; j++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      for(mi=1; mi<= wav[i]-1; mi++){
             ij++;        for (ii=1;ii<=nlstate+ndeath;ii++)
           }          for (j=1;j<=nlstate+ndeath;j++){
           else            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }          }
           fprintf(ficgp,")");        for(d=0; d<dh[mi][i]; d++){
         }          newm=savm;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          for (kk=1; kk<=cptcovage;kk++) {
         i=i+ncovmodel;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        }          }
      }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
    }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    }          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
              /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   fclose(ficgp);          savm=oldm;
 }  /* end gnuplot */          oldm=newm;
         } /* end mult */
         
 /*************** Moving average **************/        s1=s[mw[mi][i]][i];
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
   int i, cpt, cptcod;        /* bias is positive if real duration
     for (agedeb=agemin; agedeb<=fage; agedeb++)         * is higher than the multiple of stepm and negative otherwise.
       for (i=1; i<=nlstate;i++)         */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           mobaverage[(int)agedeb][i][cptcod]=0.;          lli=log(out[s1][s2] - savm[s1][s2]);
            } else if  (s2==-2) {
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){          for (j=1,survp=0. ; j<=nlstate; j++) 
       for (i=1; i<=nlstate;i++){            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          lli= log(survp);
           for (cpt=0;cpt<=4;cpt++){        }else if (mle==1){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           }        } else if(mle==2){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          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 */
         }        } else if(mle==3){  /* exponential inter-extrapolation */
       }          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     }        } else if (mle==4){  /* mle=4 no inter-extrapolation */
              lli=log(out[s1][s2]); /* Original formula */
 }        } else{  /* mle=0 back to 1 */
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
 /************** Forecasting ******************/        } /* End of if */
 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){        ipmx +=1;
          sw += weight[i];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int *popage;        /*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]); */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        if(globpr){
   double *popeffectif,*popcount;          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   double ***p3mat;   %11.6f %11.6f %11.6f ", \
   char fileresf[FILENAMELENGTH];                  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]);
  agelim=AGESUP;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          }
            fprintf(ficresilk," %10.6f\n", -llt);
          }
   strcpy(fileresf,"f");      } /* end of wave */
   strcat(fileresf,fileres);    } /* end of individual */
   if((ficresf=fopen(fileresf,"w"))==NULL) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     printf("Problem with forecast resultfile: %s\n", fileresf);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   printf("Computing forecasting: result on file '%s' \n", fileresf);    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      gsw=sw;
     }
   if (mobilav==1) {    return -l;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
     movingaverage(agedeb, fage, agemin, mobaverage);  
   }  
   /*************** function likelione ***********/
   stepsize=(int) (stepm+YEARM-1)/YEARM;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   if (stepm<=12) stepsize=1;  {
      /* This routine should help understanding what is done with 
   agelim=AGESUP;       the selection of individuals/waves and
         to check the exact contribution to the likelihood.
   hstepm=1;       Plotting could be done.
   hstepm=hstepm/stepm;     */
   yp1=modf(dateintmean,&yp);    int k;
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);    if(*globpri !=0){ /* Just counts and sums, no printings */
   mprojmean=yp;      strcpy(fileresilk,"ilk"); 
   yp1=modf((yp2*30.5),&yp);      strcat(fileresilk,fileres);
   jprojmean=yp;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   if(jprojmean==0) jprojmean=1;        printf("Problem with resultfile: %s\n", fileresilk);
   if(mprojmean==0) jprojmean=1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
        }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   for(cptcov=1;cptcov<=i2;cptcov++){      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(k=1; k<=nlstate; k++) 
       k=k+1;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresf,"\n#******");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       for(j=1;j<=cptcoveff;j++) {    }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }    *fretone=(*funcone)(p);
       fprintf(ficresf,"******\n");    if(*globpri !=0){
       fprintf(ficresf,"# StartingAge FinalAge");      fclose(ficresilk);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
            fflush(fichtm); 
          } 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    return;
         fprintf(ficresf,"\n");  }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  /*********** Maximum Likelihood Estimation ***************/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
            {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i,j, iter=0;
           oldm=oldms;savm=savms;    double **xi;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double fret;
            double fretone; /* Only one call to likelihood */
           for (h=0; h<=nhstepm; h++){    /*  char filerespow[FILENAMELENGTH];*/
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);  #ifdef NLOPT
             }    int creturn;
             for(j=1; j<=nlstate+ndeath;j++) {    nlopt_opt opt;
               kk1=0.;kk2=0;    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
               for(i=1; i<=nlstate;i++) {                  double *lb;
                 if (mobilav==1)    double minf; /* the minimum objective value, upon return */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    double * p1; /* Shifted parameters from 0 instead of 1 */
                 else {    myfunc_data dinst, *d = &dinst;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  #endif
                 }  
                  
               }    xi=matrix(1,npar,1,npar);
               if (h==(int)(calagedate+12*cpt)){    for (i=1;i<=npar;i++)
                 fprintf(ficresf," %.3f", kk1);      for (j=1;j<=npar;j++)
                                xi[i][j]=(i==j ? 1.0 : 0.0);
               }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
             }    strcpy(filerespow,"pow"); 
           }    strcat(filerespow,fileres);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         }      printf("Problem with resultfile: %s\n", filerespow);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }    }
   }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
            for (i=1;i<=nlstate;i++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fclose(ficresf);    fprintf(ficrespow,"\n");
 }  #ifdef POWELL
 /************** Forecasting ******************/    powell(p,xi,npar,ftol,&iter,&fret,func);
 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
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  #ifdef NLOPT
   int *popage;  #ifdef NEWUOA
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   double *popeffectif,*popcount;  #else
   double ***p3mat,***tabpop,***tabpopprev;    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   char filerespop[FILENAMELENGTH];  #endif
     lb=vector(0,npar-1);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    nlopt_set_lower_bounds(opt, lb);
   agelim=AGESUP;    nlopt_set_initial_step1(opt, 0.1);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    
      p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    d->function = func;
      printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
      nlopt_set_min_objective(opt, myfunc, d);
   strcpy(filerespop,"pop");    nlopt_set_xtol_rel(opt, ftol);
   strcat(filerespop,fileres);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      printf("nlopt failed! %d\n",creturn); 
     printf("Problem with forecast resultfile: %s\n", filerespop);    }
   }    else {
   printf("Computing forecasting: result on file '%s' \n", filerespop);      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);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      iter=1; /* not equal */
     }
   if (mobilav==1) {    nlopt_destroy(opt);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  #endif
     movingaverage(agedeb, fage, agemin, mobaverage);    free_matrix(xi,1,npar,1,npar);
   }    fclose(ficrespow);
     printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   if (stepm<=12) stepsize=1;    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
    
   agelim=AGESUP;  }
    
   hstepm=1;  /**** Computes Hessian and covariance matrix ***/
   hstepm=hstepm/stepm;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    {
   if (popforecast==1) {    double  **a,**y,*x,pd;
     if((ficpop=fopen(popfile,"r"))==NULL) {    double **hess;
       printf("Problem with population file : %s\n",popfile);exit(0);    int i, j;
     }    int *indx;
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     popcount=vector(0,AGESUP);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
        void lubksb(double **a, int npar, int *indx, double b[]) ;
     i=1;      void ludcmp(double **a, int npar, int *indx, double *d) ;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    double gompertz(double p[]);
        hess=matrix(1,npar,1,npar);
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    printf("\nCalculation of the hessian matrix. Wait...\n");
   }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
   for(cptcov=1;cptcov<=i2;cptcov++){      printf("%d",i);fflush(stdout);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficlog,"%d",i);fflush(ficlog);
       k=k+1;     
       fprintf(ficrespop,"\n#******");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(j=1;j<=cptcoveff;j++) {      
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /*  printf(" %f ",p[i]);
       }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       fprintf(ficrespop,"******\n");    }
       fprintf(ficrespop,"# Age");    
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    for (i=1;i<=npar;i++) {
       if (popforecast==1)  fprintf(ficrespop," [Population]");      for (j=1;j<=npar;j++)  {
              if (j>i) { 
       for (cpt=0; cpt<=0;cpt++) {          printf(".%d%d",i,j);fflush(stdout);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                  hess[i][j]=hessij(p,delti,i,j,func,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){          
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          hess[j][i]=hess[i][j];    
           nhstepm = nhstepm/hstepm;          /*printf(" %lf ",hess[i][j]);*/
                  }
           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);      printf("\n");
            fprintf(ficlog,"\n");
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
             }    
             for(j=1; j<=nlstate+ndeath;j++) {    a=matrix(1,npar,1,npar);
               kk1=0.;kk2=0;    y=matrix(1,npar,1,npar);
               for(i=1; i<=nlstate;i++) {                  x=vector(1,npar);
                 if (mobilav==1)    indx=ivector(1,npar);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    for (i=1;i<=npar;i++)
                 else {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    ludcmp(a,npar,indx,&pd);
                 }  
               }    for (j=1;j<=npar;j++) {
               if (h==(int)(calagedate+12*cpt)){      for (i=1;i<=npar;i++) x[i]=0;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      x[j]=1;
                   /*fprintf(ficrespop," %.3f", kk1);      lubksb(a,npar,indx,x);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      for (i=1;i<=npar;i++){ 
               }        matcov[i][j]=x[i];
             }      }
             for(i=1; i<=nlstate;i++){    }
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){    printf("\n#Hessian matrix#\n");
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    fprintf(ficlog,"\n#Hessian matrix#\n");
                 }    for (i=1;i<=npar;i++) { 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      for (j=1;j<=npar;j++) { 
             }        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      printf("\n");
           }      fprintf(ficlog,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
         }  
       }    /* Recompute Inverse */
      for (i=1;i<=npar;i++)
   /******/      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /*  printf("\n#Hessian matrix recomputed#\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for (j=1;j<=npar;j++) {
           nhstepm = nhstepm/hstepm;      for (i=1;i<=npar;i++) x[i]=0;
                x[j]=1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      lubksb(a,npar,indx,x);
           oldm=oldms;savm=savms;      for (i=1;i<=npar;i++){ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          y[i][j]=x[i];
           for (h=0; h<=nhstepm; h++){        printf("%.3e ",y[i][j]);
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficlog,"%.3e ",y[i][j]);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      }
             }      printf("\n");
             for(j=1; j<=nlstate+ndeath;j++) {      fprintf(ficlog,"\n");
               kk1=0.;kk2=0;    }
               for(i=1; i<=nlstate;i++) {                  */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }    free_matrix(a,1,npar,1,npar);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    free_matrix(y,1,npar,1,npar);
             }    free_vector(x,1,npar);
           }    free_ivector(indx,1,npar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(hess,1,npar,1,npar);
         }  
       }  
    }  }
   }  
    /*************** hessian matrix ****************/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
   if (popforecast==1) {    int i;
     free_ivector(popage,0,AGESUP);    int l=1, lmax=20;
     free_vector(popeffectif,0,AGESUP);    double k1,k2;
     free_vector(popcount,0,AGESUP);    double p2[MAXPARM+1]; /* identical to x */
   }    double res;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double fx;
   fclose(ficrespop);    int k=0,kmax=10;
 }    double l1;
   
 /***********************************************/    fx=func(x);
 /**************** Main Program *****************/    for (i=1;i<=npar;i++) p2[i]=x[i];
 /***********************************************/    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       l1=pow(10,l);
 int main(int argc, char *argv[])      delts=delt;
 {      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        p2[theta]=x[theta] +delt;
   double agedeb, agefin,hf;        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
   double fret;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   double **xi,tmp,delta;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   double dum; /* Dummy variable */  #ifdef DEBUGHESS
   double ***p3mat;        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);
   int *indx;        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);
   char line[MAXLINE], linepar[MAXLINE];  #endif
   char title[MAXLINE];        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          k=kmax;
          }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10;
   char filerest[FILENAMELENGTH];        }
   char fileregp[FILENAMELENGTH];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   char popfile[FILENAMELENGTH];          delts=delt;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        }
   int firstobs=1, lastobs=10;      }
   int sdeb, sfin; /* Status at beginning and end */    }
   int c,  h , cpt,l;    delti[theta]=delts;
   int ju,jl, mi;    return res; 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  }
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;  {
     int i;
   double bage, fage, age, agelim, agebase;    int l=1, lmax=20;
   double ftolpl=FTOL;    double k1,k2,k3,k4,res,fx;
   double **prlim;    double p2[MAXPARM+1];
   double *severity;    int k;
   double ***param; /* Matrix of parameters */  
   double  *p;    fx=func(x);
   double **matcov; /* Matrix of covariance */    for (k=1; k<=2; k++) {
   double ***delti3; /* Scale */      for (i=1;i<=npar;i++) p2[i]=x[i];
   double *delti; /* Scale */      p2[thetai]=x[thetai]+delti[thetai]/k;
   double ***eij, ***vareij;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double **varpl; /* Variances of prevalence limits by age */      k1=func(p2)-fx;
   double *epj, vepp;    
   double kk1, kk2;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
     
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";      p2[thetai]=x[thetai]-delti[thetai]/k;
   char *alph[]={"a","a","b","c","d","e"}, str[4];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
     
   char z[1]="c", occ;      p2[thetai]=x[thetai]-delti[thetai]/k;
 #include <sys/time.h>      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 #include <time.h>      k4=func(p2)-fx;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    #ifdef DEBUG
   /* long total_usecs;      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);
   struct timeval start_time, end_time;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
    #endif
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    }
     return res;
   }
   printf("\n%s",version);  
   if(argc <=1){  /************** Inverse of matrix **************/
     printf("\nEnter the parameter file name: ");  void ludcmp(double **a, int n, int *indx, double *d) 
     scanf("%s",pathtot);  { 
   }    int i,imax,j,k; 
   else{    double big,dum,sum,temp; 
     strcpy(pathtot,argv[1]);    double *vv; 
   }   
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    vv=vector(1,n); 
   /*cygwin_split_path(pathtot,path,optionfile);    *d=1.0; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for (i=1;i<=n;i++) { 
   /* cutv(path,optionfile,pathtot,'\\');*/      big=0.0; 
       for (j=1;j<=n;j++) 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        if ((temp=fabs(a[i][j])) > big) big=temp; 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   chdir(path);      vv[i]=1.0/big; 
   replace(pathc,path);    } 
     for (j=1;j<=n;j++) { 
 /*-------- arguments in the command line --------*/      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
   strcpy(fileres,"r");        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   strcat(fileres, optionfilefiname);        a[i][j]=sum; 
   strcat(fileres,".txt");    /* Other files have txt extension */      } 
       big=0.0; 
   /*---------arguments file --------*/      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for (k=1;k<j;k++) 
     printf("Problem with optionfile %s\n",optionfile);          sum -= a[i][k]*a[k][j]; 
     goto end;        a[i][j]=sum; 
   }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
   strcpy(filereso,"o");          imax=i; 
   strcat(filereso,fileres);        } 
   if((ficparo=fopen(filereso,"w"))==NULL) {      } 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      if (j != imax) { 
   }        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
   /* Reads comments: lines beginning with '#' */          a[imax][k]=a[j][k]; 
   while((c=getc(ficpar))=='#' && c!= EOF){          a[j][k]=dum; 
     ungetc(c,ficpar);        } 
     fgets(line, MAXLINE, ficpar);        *d = -(*d); 
     puts(line);        vv[imax]=vv[j]; 
     fputs(line,ficparo);      } 
   }      indx[j]=imax; 
   ungetc(c,ficpar);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
   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);        dum=1.0/(a[j][j]); 
   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);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   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){    } 
     ungetc(c,ficpar);    free_vector(vv,1,n);  /* Doesn't work */
     fgets(line, MAXLINE, ficpar);  ;
     puts(line);  } 
     fputs(line,ficparo);  
   }  void lubksb(double **a, int n, int *indx, double b[]) 
   ungetc(c,ficpar);  { 
      int i,ii=0,ip,j; 
        double sum; 
   covar=matrix(0,NCOVMAX,1,n);   
   cptcovn=0;    for (i=1;i<=n;i++) { 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      ip=indx[i]; 
       sum=b[ip]; 
   ncovmodel=2+cptcovn;      b[ip]=b[i]; 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      if (ii) 
          for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   /* Read guess parameters */      else if (sum) ii=i; 
   /* Reads comments: lines beginning with '#' */      b[i]=sum; 
   while((c=getc(ficpar))=='#' && c!= EOF){    } 
     ungetc(c,ficpar);    for (i=n;i>=1;i--) { 
     fgets(line, MAXLINE, ficpar);      sum=b[i]; 
     puts(line);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     fputs(line,ficparo);      b[i]=sum/a[i][i]; 
   }    } 
   ungetc(c,ficpar);  } 
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  void pstamp(FILE *fichier)
     for(i=1; i <=nlstate; i++)  {
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  }
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);  /************ Frequencies ********************/
       for(k=1; k<=ncovmodel;k++){  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[])
         fscanf(ficpar," %lf",&param[i][j][k]);  {  /* Some frequencies */
         printf(" %lf",param[i][j][k]);    
         fprintf(ficparo," %lf",param[i][j][k]);    int i, m, jk, j1, bool, z1,j;
       }    int first;
       fscanf(ficpar,"\n");    double ***freq; /* Frequencies */
       printf("\n");    double *pp, **prop;
       fprintf(ficparo,"\n");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     }    char fileresp[FILENAMELENGTH];
      
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
   p=param[1][1];    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
   /* Reads comments: lines beginning with '#' */    if((ficresp=fopen(fileresp,"w"))==NULL) {
   while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with prevalence resultfile: %s\n", fileresp);
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     fgets(line, MAXLINE, ficpar);      exit(0);
     puts(line);    }
     fputs(line,ficparo);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   }    j1=0;
   ungetc(c,ficpar);    
     j=cptcoveff;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){    first=1;
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
       printf("%1d%1d",i,j);    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
       fprintf(ficparo,"%1d%1d",i1,j1);    /*    j1++; */
       for(k=1; k<=ncovmodel;k++){    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         printf(" %le",delti3[i][j][k]);          scanf("%d", i);*/
         fprintf(ficparo," %le",delti3[i][j][k]);        for (i=-5; i<=nlstate+ndeath; i++)  
       }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       fscanf(ficpar,"\n");            for(m=iagemin; m <= iagemax+3; m++)
       printf("\n");              freq[i][jk][m]=0;
       fprintf(ficparo,"\n");        
     }        for (i=1; i<=nlstate; i++)  
   }          for(m=iagemin; m <= iagemax+3; m++)
   delti=delti3[1][1];            prop[i][m]=0;
          
   /* Reads comments: lines beginning with '#' */        dateintsum=0;
   while((c=getc(ficpar))=='#' && c!= EOF){        k2cpt=0;
     ungetc(c,ficpar);        for (i=1; i<=imx; i++) {
     fgets(line, MAXLINE, ficpar);          bool=1;
     puts(line);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
     fputs(line,ficparo);            for (z1=1; z1<=cptcoveff; z1++)       
   }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
   ungetc(c,ficpar);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                  bool=0;
   matcov=matrix(1,npar,1,npar);                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
   for(i=1; i <=npar; i++){                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
     fscanf(ficpar,"%s",&str);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
     printf("%s",str);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
     fprintf(ficparo,"%s",str);              } 
     for(j=1; j <=i; j++){          }
       fscanf(ficpar," %le",&matcov[i][j]);   
       printf(" %.5le",matcov[i][j]);          if (bool==1){
       fprintf(ficparo," %.5le",matcov[i][j]);            for(m=firstpass; m<=lastpass; m++){
     }              k2=anint[m][i]+(mint[m][i]/12.);
     fscanf(ficpar,"\n");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     printf("\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(ficparo,"\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   for(i=1; i <=npar; i++)                if (m<lastpass) {
     for(j=i+1;j<=npar;j++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       matcov[i][j]=matcov[j][i];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                    }
   printf("\n");                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
     /*-------- data file ----------*/                  k2cpt++;
     if((ficres =fopen(fileres,"w"))==NULL) {                }
       printf("Problem with resultfile: %s\n", fileres);goto end;                /*}*/
     }            }
     fprintf(ficres,"#%s\n",version);          }
            } /* end i */
     if((fic=fopen(datafile,"r"))==NULL)    {         
       printf("Problem with datafile: %s\n", datafile);goto end;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     }        pstamp(ficresp);
         if  (cptcovn>0) {
     n= lastobs;          fprintf(ficresp, "\n#********** Variable "); 
     severity = vector(1,maxwav);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     outcome=imatrix(1,maxwav+1,1,n);          fprintf(ficresp, "**********\n#");
     num=ivector(1,n);          fprintf(ficlog, "\n#********** Variable "); 
     moisnais=vector(1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     annais=vector(1,n);          fprintf(ficlog, "**********\n#");
     moisdc=vector(1,n);        }
     andc=vector(1,n);        for(i=1; i<=nlstate;i++) 
     agedc=vector(1,n);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     cod=ivector(1,n);        fprintf(ficresp, "\n");
     weight=vector(1,n);        
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for(i=iagemin; i <= iagemax+3; i++){
     mint=matrix(1,maxwav,1,n);          if(i==iagemax+3){
     anint=matrix(1,maxwav,1,n);            fprintf(ficlog,"Total");
     s=imatrix(1,maxwav+1,1,n);          }else{
     adl=imatrix(1,maxwav+1,1,n);                if(first==1){
     tab=ivector(1,NCOVMAX);              first=0;
     ncodemax=ivector(1,8);              printf("See log file for details...\n");
             }
     i=1;            fprintf(ficlog,"Age %d", i);
     while (fgets(line, MAXLINE, fic) != NULL)    {          }
       if ((i >= firstobs) && (i <=lastobs)) {          for(jk=1; jk <=nlstate ; jk++){
                    for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         for (j=maxwav;j>=1;j--){              pp[jk] += freq[jk][m][i]; 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          }
           strcpy(line,stra);          for(jk=1; jk <=nlstate ; jk++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for(m=-1, pos=0; m <=0 ; m++)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              pos += freq[jk][m][i];
         }            if(pp[jk]>=1.e-10){
                      if(first==1){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            }else{
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         for (j=ncov;j>=1;j--){            }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }
         }  
         num[i]=atol(stra);          for(jk=1; jk <=nlstate ; jk++){
                    for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              pp[jk] += freq[jk][m][i];
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         i=i+1;            pos += pp[jk];
       }            posprop += prop[jk][i];
     }          }
     /* printf("ii=%d", ij);          for(jk=1; jk <=nlstate ; jk++){
        scanf("%d",i);*/            if(pos>=1.e-5){
   imx=i-1; /* Number of individuals */              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   /* for (i=1; i<=imx; i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;            }else{
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              if(first==1)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
     for (i=1; i<=imx; i++)            if( i <= iagemax){
     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(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   /* Calculation of the number of parameter from char model*/                /*probs[i][jk][j1]= pp[jk]/pos;*/
   Tvar=ivector(1,15);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   Tprod=ivector(1,15);              }
   Tvaraff=ivector(1,15);              else
   Tvard=imatrix(1,15,1,2);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   Tage=ivector(1,15);                  }
              }
   if (strlen(model) >1){          
     j=0, j1=0, k1=1, k2=1;          for(jk=-1; jk <=nlstate+ndeath; jk++)
     j=nbocc(model,'+');            for(m=-1; m <=nlstate+ndeath; m++)
     j1=nbocc(model,'*');              if(freq[jk][m][i] !=0 ) {
     cptcovn=j+1;              if(first==1)
     cptcovprod=j1;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                    fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                  }
     strcpy(modelsav,model);          if(i <= iagemax)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            fprintf(ficresp,"\n");
       printf("Error. Non available option model=%s ",model);          if(first==1)
       goto end;            printf("Others in log...\n");
     }          fprintf(ficlog,"\n");
            }
     for(i=(j+1); i>=1;i--){        /*}*/
       cutv(stra,strb,modelsav,'+');    }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    dateintmean=dateintsum/k2cpt; 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/   
       /*scanf("%d",i);*/    fclose(ficresp);
       if (strchr(strb,'*')) {    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         cutv(strd,strc,strb,'*');    free_vector(pp,1,nlstate);
         if (strcmp(strc,"age")==0) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           cptcovprod--;    /* End of Freq */
           cutv(strb,stre,strd,'V');  }
           Tvar[i]=atoi(stre);  
           cptcovage++;  /************ Prevalence ********************/
             Tage[cptcovage]=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)
             /*printf("stre=%s ", stre);*/  {  
         }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         else if (strcmp(strd,"age")==0) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
           cptcovprod--;       We still use firstpass and lastpass as another selection.
           cutv(strb,stre,strc,'V');    */
           Tvar[i]=atoi(stre);   
           cptcovage++;    int i, m, jk, j1, bool, z1,j;
           Tage[cptcovage]=i;  
         }    double **prop;
         else {    double posprop; 
           cutv(strb,stre,strc,'V');    double  y2; /* in fractional years */
           Tvar[i]=ncov+k1;    int iagemin, iagemax;
           cutv(strb,strc,strd,'V');    int first; /** to stop verbosity which is redirected to log file */
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);    iagemin= (int) agemin;
           Tvard[k1][2]=atoi(stre);    iagemax= (int) agemax;
           Tvar[cptcovn+k2]=Tvard[k1][1];    /*pp=vector(1,nlstate);*/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           for (k=1; k<=lastobs;k++)    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    j1=0;
           k1++;    
           k2=k2+2;    /*j=cptcoveff;*/
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }    
       else {    first=1;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
        /*  scanf("%d",i);*/      /*for(i1=1; i1<=ncodemax[k1];i1++){
       cutv(strd,strc,strb,'V');        j1++;*/
       Tvar[i]=atoi(strc);        
       }        for (i=1; i<=nlstate; i++)  
       strcpy(modelsav,stra);            for(m=iagemin; m <= iagemax+3; m++)
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            prop[i][m]=0.0;
         scanf("%d",i);*/       
     }        for (i=1; i<=imx; i++) { /* Each individual */
 }          bool=1;
            if  (cptcovn>0) {
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            for (z1=1; z1<=cptcoveff; z1++) 
   printf("cptcovprod=%d ", cptcovprod);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   scanf("%d ",i);*/                bool=0;
     fclose(fic);          } 
           if (bool==1) { 
     /*  if(mle==1){*/            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     if (weightopt != 1) { /* Maximisation without weights*/              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for(i=1;i<=n;i++) weight[i]=1.0;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     /*-calculation of age at interview from date of interview and age at death -*/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     agev=matrix(1,maxwav,1,imx);                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) { 
    for (i=1; i<=imx; i++)                  /*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]]);*/
      for(m=2; (m<= maxwav); m++)                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                  prop[s[m][i]][iagemax+3] += weight[i]; 
          anint[m][i]=9999;                } 
          s[m][i]=-1;              }
        }            } /* end selection of waves */
              }
     for (i=1; i<=imx; i++)  {        }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for(i=iagemin; i <= iagemax+3; i++){  
       for(m=1; (m<= maxwav); m++){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         if(s[m][i] >0){            posprop += prop[jk][i]; 
           if (s[m][i] == nlstate+1) {          } 
             if(agedc[i]>0)          
               if(moisdc[i]!=99 && andc[i]!=9999)          for(jk=1; jk <=nlstate ; jk++){     
               agev[m][i]=agedc[i];            if( i <=  iagemax){ 
             else {              if(posprop>=1.e-5){ 
               if (andc[i]!=9999){                probs[i][jk][j1]= prop[jk][i]/posprop;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              } else{
               agev[m][i]=-1;                if(first==1){
               }                  first=0;
             }                  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]);
           }                }
           else if(s[m][i] !=9){ /* Should no more exist */              }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            } 
             if(mint[m][i]==99 || anint[m][i]==9999)          }/* end jk */ 
               agev[m][i]=1;        }/* end i */ 
             else if(agev[m][i] <agemin){      /*} *//* end i1 */
               agemin=agev[m][i];    } /* end j1 */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    
             }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
             else if(agev[m][i] >agemax){    /*free_vector(pp,1,nlstate);*/
               agemax=agev[m][i];    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  }  /* End of prevalence */
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/  /************* Waves Concatenation ***************/
             /*   agev[m][i] = age[i]+2*m;*/  
           }  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)
           else { /* =9 */  {
             agev[m][i]=1;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
             s[m][i]=-1;       Death is a valid wave (if date is known).
           }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         else /*= 0 Unknown */       and mw[mi+1][i]. dh depends on stepm.
           agev[m][i]=1;       */
       }  
        int i, mi, m;
     }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for (i=1; i<=imx; i++)  {       double sum=0., jmean=0.;*/
       for(m=1; (m<= maxwav); m++){    int first;
         if (s[m][i] > (nlstate+ndeath)) {    int j, k=0,jk, ju, jl;
           printf("Error: Wrong value in nlstate or ndeath\n");      double sum=0.;
           goto end;    first=0;
         }    jmin=100000;
       }    jmax=-1;
     }    jmean=0.;
     for(i=1; i<=imx; i++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      mi=0;
       m=firstpass;
     free_vector(severity,1,maxwav);      while(s[m][i] <= nlstate){
     free_imatrix(outcome,1,maxwav+1,1,n);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     free_vector(moisnais,1,n);          mw[++mi][i]=m;
     free_vector(annais,1,n);        if(m >=lastpass)
     /* free_matrix(mint,1,maxwav,1,n);          break;
        free_matrix(anint,1,maxwav,1,n);*/        else
     free_vector(moisdc,1,n);          m++;
     free_vector(andc,1,n);      }/* end while */
       if (s[m][i] > nlstate){
            mi++;     /* Death is another wave */
     wav=ivector(1,imx);        /* if(mi==0)  never been interviewed correctly before death */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);           /* Only death is a correct wave */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        mw[mi][i]=m;
          }
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      wav[i]=mi;
       if(mi==0){
         nbwarn++;
       Tcode=ivector(1,100);        if(first==0){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       ncodemax[1]=1;          first=1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        }
              if(first==1){
    codtab=imatrix(1,100,1,10);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
    h=0;        }
    m=pow(2,cptcoveff);      } /* end mi==0 */
      } /* End individuals */
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    for(i=1; i<=imx; i++){
        for(j=1; j <= ncodemax[k]; j++){      for(mi=1; mi<wav[i];mi++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        if (stepm <=0)
            h++;          dh[mi][i]=1;
            if (h>m) h=1;codtab[h][k]=j;        else{
          }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
        }            if (agedc[i] < 2*AGESUP) {
      }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
    }              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
                 nberr++;
    /*for(i=1; i <=m ;i++){                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(k=1; k <=cptcovn; k++){                j=1; /* Temporary Dangerous patch */
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
      }                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      printf("\n");                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);
    }              }
    scanf("%d",i);*/              k=k+1;
                  if (j >= jmax){
    /* Calculates basic frequencies. Computes observed prevalence at single age                jmax=j;
        and prints on file fileres'p'. */                ijmax=i;
               }
                  if (j <= jmin){
                    jmin=j;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                ijmin=i;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              sum=sum+j;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                  }
     /* For Powell, parameters are in a vector p[] starting at p[1]          }
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          else{
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            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]); */
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            k=k+1;
     }            if (j >= jmax) {
                  jmax=j;
     /*--------- results files --------------*/              ijmax=i;
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);            }
              else if (j <= jmin){
               jmin=j;
    jk=1;              ijmin=i;
    fprintf(ficres,"# Parameters\n");            }
    printf("# Parameters\n");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
    for(i=1,jk=1; i <=nlstate; 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]);*/
      for(k=1; k <=(nlstate+ndeath); k++){            if(j<0){
        if (k != i)              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]);
            printf("%d%d ",i,k);              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]);
            fprintf(ficres,"%1d%1d ",i,k);            }
            for(j=1; j <=ncovmodel; j++){            sum=sum+j;
              printf("%f ",p[jk]);          }
              fprintf(ficres,"%f ",p[jk]);          jk= j/stepm;
              jk++;          jl= j -jk*stepm;
            }          ju= j -(jk+1)*stepm;
            printf("\n");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
            fprintf(ficres,"\n");            if(jl==0){
          }              dh[mi][i]=jk;
      }              bh[mi][i]=0;
    }            }else{ /* We want a negative bias in order to only have interpolation ie
  if(mle==1){                    * to avoid the price of an extra matrix product in likelihood */
     /* Computing hessian and covariance matrix */              dh[mi][i]=jk+1;
     ftolhess=ftol; /* Usually correct */              bh[mi][i]=ju;
     hesscov(matcov, p, npar, delti, ftolhess, func);            }
  }          }else{
     fprintf(ficres,"# Scales\n");            if(jl <= -ju){
     printf("# Scales\n");              dh[mi][i]=jk;
      for(i=1,jk=1; i <=nlstate; i++){              bh[mi][i]=jl;       /* bias is positive if real duration
       for(j=1; j <=nlstate+ndeath; j++){                                   * is higher than the multiple of stepm and negative otherwise.
         if (j!=i) {                                   */
           fprintf(ficres,"%1d%1d",i,j);            }
           printf("%1d%1d",i,j);            else{
           for(k=1; k<=ncovmodel;k++){              dh[mi][i]=jk+1;
             printf(" %.5e",delti[jk]);              bh[mi][i]=ju;
             fprintf(ficres," %.5e",delti[jk]);            }
             jk++;            if(dh[mi][i]==0){
           }              dh[mi][i]=1; /* At least one step */
           printf("\n");              bh[mi][i]=ju; /* At least one step */
           fprintf(ficres,"\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);*/
         }            }
       }          } /* end if mle */
      }        }
          } /* end wave */
     k=1;    }
     fprintf(ficres,"# Covariance\n");    jmean=sum/k;
     printf("# Covariance\n");    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);
     for(i=1;i<=npar;i++){    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);
       /*  if (k>nlstate) k=1;   }
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  /*********** Tricode ****************************/
       printf("%s%d%d",alph[k],i1,tab[i]);*/  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
       fprintf(ficres,"%3d",i);  {
       printf("%3d",i);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       for(j=1; j<=i;j++){    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
         fprintf(ficres," %.5e",matcov[i][j]);     * Boring subroutine which should only output nbcode[Tvar[j]][k]
         printf(" %.5e",matcov[i][j]);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       }     * nbcode[Tvar[j]][1]= 
       fprintf(ficres,"\n");    */
       printf("\n");  
       k++;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     }    int modmaxcovj=0; /* Modality max of covariates j */
        int cptcode=0; /* Modality max of covariates j */
     while((c=getc(ficpar))=='#' && c!= EOF){    int modmincovj=0; /* Modality min of covariates j */
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  
       puts(line);    cptcoveff=0; 
       fputs(line,ficparo);   
     }    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     ungetc(c,ficpar);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);    /* Loop on covariates without age and products */
        for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
     if (fage <= 2) {      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
       bage = agemin;                                 modality of this covariate Vj*/ 
       fage = agemaxpar;        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
     }                                      * If product of Vn*Vm, still boolean *:
                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);                                        modality of the nth covariate of individual i. */
          if (ij > modmaxcovj)
     while((c=getc(ficpar))=='#' && c!= EOF){          modmaxcovj=ij; 
     ungetc(c,ficpar);        else if (ij < modmincovj) 
     fgets(line, MAXLINE, ficpar);          modmincovj=ij; 
     puts(line);        if ((ij < -1) && (ij > NCOVMAX)){
     fputs(line,ficparo);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   }          exit(1);
   ungetc(c,ficpar);        }else
          Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /* 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]);
         if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        }
         /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
   fscanf(ficpar,"pop_based=%d\n",&popbased);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
   fprintf(ficparo,"pop_based=%d\n",popbased);        } /* Ndum[-1] number of undefined modalities */
   fprintf(ficres,"pop_based=%d\n",popbased);    
        /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   while((c=getc(ficpar))=='#' && c!= EOF){      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
     ungetc(c,ficpar);      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
     fgets(line, MAXLINE, ficpar);         modmincovj=3; modmaxcovj = 7;
     puts(line);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
     fputs(line,ficparo);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
   }         variables V1_1 and V1_2.
   ungetc(c,ficpar);         nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
   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);         nbcode[Tvar[j]][2]=1;
 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);         nbcode[Tvar[j]][3]=2;
 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);      */
       ij=1; /* ij is similar to i but can jumps over null modalities */
       for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
 while((c=getc(ficpar))=='#' && c!= EOF){        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
     ungetc(c,ficpar);          /*recode from 0 */
     fgets(line, MAXLINE, ficpar);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
     puts(line);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     fputs(line,ficparo);                                       k is a modality. If we have model=V1+V1*sex 
   }                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   ungetc(c,ficpar);            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);          if (ij > ncodemax[j]) break; 
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }  /* end of loop on */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      } /* 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*/  
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
 /*------------ gnuplot -------------*/    
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
       /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
 /*------------ free_vector  -------------*/     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
  chdir(path);     Ndum[ij]++; 
     } 
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);   ij=1;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);     for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
  free_ivector(num,1,n);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
  free_vector(agedc,1,n);     if((Ndum[i]!=0) && (i<=ncovcol)){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
  fclose(ficparo);       Tvaraff[ij]=i; /*For printing (unclear) */
  fclose(ficres);       ij++;
      }else
 /*--------- index.htm --------*/         Tvaraff[ij]=0;
    }
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);   ij--;
    cptcoveff=ij; /*Number of total covariates*/
    
   /*--------------- Prevalence limit --------------*/  }
    
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);  /*********** Health Expectancies ****************/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  {
   fprintf(ficrespl,"#Prevalence limit\n");    /* Health expectancies, no variances */
   fprintf(ficrespl,"#Age ");    int i, j, nhstepm, hstepm, h, nstepm;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    int nhstepma, nstepma; /* Decreasing with age */
   fprintf(ficrespl,"\n");    double age, agelim, hf;
      double ***p3mat;
   prlim=matrix(1,nlstate,1,nlstate);    double eip;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficreseij);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficreseij,"# Age");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    for(i=1; i<=nlstate;i++){
   k=0;      for(j=1; j<=nlstate;j++){
   agebase=agemin;        fprintf(ficreseij," e%1d%1d ",i,j);
   agelim=agemaxpar;      }
   ftolpl=1.e-10;      fprintf(ficreseij," e%1d. ",i);
   i1=cptcoveff;    }
   if (cptcovn < 1){i1=1;}    fprintf(ficreseij,"\n");
   
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if(estepm < stepm){
         k=k+1;      printf ("Problem %d lower than %d\n",estepm, stepm);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    }
         fprintf(ficrespl,"\n#******");    else  hstepm=estepm;   
         for(j=1;j<=cptcoveff;j++)    /* We compute the life expectancy from trapezoids spaced every estepm months
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * This is mainly to measure the difference between two models: for example
         fprintf(ficrespl,"******\n");     * if stepm=24 months pijx are given only every 2 years and by summing them
             * we are calculating an estimate of the Life Expectancy assuming a linear 
         for (age=agebase; age<=agelim; age++){     * progression in between and thus overestimating or underestimating according
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficrespl,"%.0f",age );     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           for(i=1; i<=nlstate;i++)     * to compare the new estimate of Life expectancy with the same linear 
           fprintf(ficrespl," %.5f", prlim[i][i]);     * hypothesis. A more precise result, taking into account a more precise
           fprintf(ficrespl,"\n");     * curvature will be obtained if estepm is as small as stepm. */
         }  
       }    /* For example we decided to compute the life expectancy with the smallest unit */
     }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   fclose(ficrespl);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   /*------------- h Pij x at various ages ------------*/       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if((ficrespij=fopen(filerespij,"w"))==NULL) {       survival function given by stepm (the optimization length). Unfortunately it
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       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 
   printf("Computing pij: result on file '%s' \n", filerespij);       results. So we changed our mind and took the option of the best precision.
      */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   /*if (stepm<=24) stepsize=2;*/  
     agelim=AGESUP;
   agelim=AGESUP;    /* If stepm=6 months */
   hstepm=stepsize*YEARM; /* Every year of age */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        
   k=0;  /* nhstepm age range expressed in number of stepm */
   for(cptcov=1;cptcov<=i1;cptcov++){    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       k=k+1;    /* if (stepm >= YEARM) hstepm=1;*/
         fprintf(ficrespij,"\n#****** ");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         for(j=1;j<=cptcoveff;j++)    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");    for (age=bage; age<=fage; age ++){ 
              nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /* if (stepm >= YEARM) hstepm=1;*/
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      /* If stepm=6 months */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /* Computed by stepm unit matrices, product of hstepma matrices, stored
           fprintf(ficrespij,"# Age");         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           for(i=1; i<=nlstate;i++)      
             for(j=1; j<=nlstate+ndeath;j++)      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
               fprintf(ficrespij," %1d-%1d",i,j);      
           fprintf(ficrespij,"\n");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           for (h=0; h<=nhstepm; h++){      
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      printf("%d|",(int)age);fflush(stdout);
             for(i=1; i<=nlstate;i++)      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
               for(j=1; j<=nlstate+ndeath;j++)      
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      /* Computing expectancies */
             fprintf(ficrespij,"\n");      for(i=1; i<=nlstate;i++)
           }        for(j=1; j<=nlstate;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           fprintf(ficrespij,"\n");            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]);*/
   }  
           }
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  
       fprintf(ficreseij,"%3.0f",age );
   fclose(ficrespij);      for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
   /*---------- Forecasting ------------------*/          eip +=eij[i][j][(int)age];
   if(stepm == 1) {          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        }
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        fprintf(ficreseij,"%9.4f", eip );
     free_matrix(mint,1,maxwav,1,n);      }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      fprintf(ficreseij,"\n");
     free_vector(weight,1,n);}      
   else{    }
     erreur=108;    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);    printf("\n");
   }    fprintf(ficlog,"\n");
      
   }
   /*---------- Health expectancies and variances ------------*/  
   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[] )
   strcpy(filerest,"t");  
   strcat(filerest,fileres);  {
   if((ficrest=fopen(filerest,"w"))==NULL) {    /* Covariances of health expectancies eij and of total life expectancies according
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;     to initial status i, ei. .
   }    */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   strcpy(filerese,"e");    double ***p3matp, ***p3matm, ***varhe;
   strcat(filerese,fileres);    double **dnewm,**doldm;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    double *xp, *xm;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double **gp, **gm;
   }    double ***gradg, ***trgradg;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    int theta;
   
  strcpy(fileresv,"v");    double eip, vip;
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    xp=vector(1,npar);
   }    xm=vector(1,npar);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    pstamp(ficresstdeij);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
       k=k+1;    fprintf(ficresstdeij,"# Age");
       fprintf(ficrest,"\n#****** ");    for(i=1; i<=nlstate;i++){
       for(j=1;j<=cptcoveff;j++)      for(j=1; j<=nlstate;j++)
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficrest,"******\n");      fprintf(ficresstdeij," e%1d. ",i);
     }
       fprintf(ficreseij,"\n#****** ");    fprintf(ficresstdeij,"\n");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    pstamp(ficrescveij);
       fprintf(ficreseij,"******\n");    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
       fprintf(ficresvij,"\n#****** ");    for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)      for(j=1; j<=nlstate;j++){
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        cptj= (j-1)*nlstate+i;
       fprintf(ficresvij,"******\n");        for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            cptj2= (j2-1)*nlstate+i2;
       oldm=oldms;savm=savms;            if(cptj2 <= cptj)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          }
       oldm=oldms;savm=savms;      }
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fprintf(ficrescveij,"\n");
        
     if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    else  hstepm=estepm;   
       fprintf(ficrest,"\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
       hf=1;     * if stepm=24 months pijx are given only every 2 years and by summing them
       if (stepm >= YEARM) hf=stepm/YEARM;     * we are calculating an estimate of the Life Expectancy assuming a linear 
       epj=vector(1,nlstate+1);     * progression in between and thus overestimating or underestimating according
       for(age=bage; age <=fage ;age++){     * to the curvature of the survival function. If, for the same date, we 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         if (popbased==1) {     * to compare the new estimate of Life expectancy with the same linear 
           for(i=1; i<=nlstate;i++)     * hypothesis. A more precise result, taking into account a more precise
             prlim[i][i]=probs[(int)age][i][k];     * curvature will be obtained if estepm is as small as stepm. */
         }  
            /* For example we decided to compute the life expectancy with the smallest unit */
         fprintf(ficrest," %.0f",age);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       nhstepm is the number of hstepm from age to agelim 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       nstepm is the number of stepm from age to agelin. 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];       Look at hpijx to understand the reason of that which relies in memory size
           }       and note for a fixed period like estepm months */
           epj[nlstate+1] +=epj[j];    /* 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
         for(i=1, vepp=0.;i <=nlstate;i++)       means that if the survival funtion is printed only each two years of age and if
           for(j=1;j <=nlstate;j++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             vepp += vareij[i][j][(int)age];       results. So we changed our mind and took the option of the best precision.
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    */
         for(j=1;j <=nlstate;j++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  
         }    /* If stepm=6 months */
         fprintf(ficrest,"\n");    /* nhstepm age range expressed in number of stepm */
       }    agelim=AGESUP;
     }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
   fclose(ficreseij);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   fclose(ficresvij);    
   fclose(ficrest);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficpar);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_vector(epj,1,nlstate+1);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   /*------- Variance limit prevalence------*/      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);    for (age=bage; age<=fage; age ++){ 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     exit(0);      /* if (stepm >= YEARM) hstepm=1;*/
   }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
       /* If stepm=6 months */
   k=0;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   for(cptcov=1;cptcov<=i1;cptcov++){         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      
       k=k+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficresvpl,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      /* Computing  Variances of health expectancies */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       fprintf(ficresvpl,"******\n");         decrease memory allocation */
            for(theta=1; theta <=npar; theta++){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        for(i=1; i<=npar; i++){ 
       oldm=oldms;savm=savms;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     }        }
  }        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   fclose(ficresvpl);    
         for(j=1; j<= nlstate; j++){
   /*---------- End : free ----------------*/          for(i=1; i<=nlstate; i++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            for(h=0; h<=nhstepm-1; h++){
                gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            }
            }
          }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(ij=1; ij<= nlstate*nlstate; ij++)
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          for(h=0; h<=nhstepm-1; h++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
            }
   free_matrix(matcov,1,npar,1,npar);      }/* End theta */
   free_vector(delti,1,npar);      
   free_matrix(agev,1,maxwav,1,imx);      
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
   if(erreur >0)          for(theta=1; theta <=npar; theta++)
     printf("End of Imach with error %d\n",erreur);            trgradg[h][j][theta]=gradg[h][theta][j];
   else   printf("End of Imach\n");      
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
         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] =0.;
   /*------ End -----------*/  
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  end:       for(h=0;h<=nhstepm-1;h++){
 #ifdef windows        for(k=0;k<=nhstepm-1;k++){
   /* chdir(pathcd);*/          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 #endif          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
  /*system("wgnuplot graph.plt");*/          for(ij=1;ij<=nlstate*nlstate;ij++)
  /*system("../gp37mgw/wgnuplot graph.plt");*/            for(ji=1;ji<=nlstate*nlstate;ji++)
  /*system("cd ../gp37mgw");*/              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        }
  strcpy(plotcmd,GNUPLOTPROGRAM);      }
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);      /* Computing expectancies */
  system(plotcmd);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
 #ifdef windows        for(j=1; j<=nlstate;j++)
   while (z[0] != 'q') {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     chdir(path);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");            
     scanf("%s",z);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') {          }
       chdir(path);  
       system(optionfilehtm);      fprintf(ficresstdeij,"%3.0f",age );
     }      for(i=1; i<=nlstate;i++){
     else if (z[0] == 'q') exit(0);        eip=0.;
   }        vip=0.;
 #endif        for(j=1; j<=nlstate;j++){
 }          eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
   
   #if defined __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
      
   
    }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.28  
changed lines
  Added in v.1.179


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