Diff for /imach/src/imach.c between versions 1.43 and 1.182

version 1.43, 2002/05/24 13:00:54 version 1.182, 2015/02/12 08:19:57
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.182  2015/02/12 08:19:57  brouard
      Summary: Trying to keep directest which seems simpler and more general
   This program computes Healthy Life Expectancies from    Author: Nicolas Brouard
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.181  2015/02/11 23:22:24  brouard
   interviewed on their health status or degree of disability (in the    Summary: Comments on Powell added
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Author:
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.180  2015/02/11 17:33:45  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.179  2015/01/04 09:57:06  brouard
   probability to be observed in state j at the second wave    Summary: back to OS/X
   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 1.178  2015/01/04 09:35:48  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    *** empty log message ***
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.177  2015/01/03 18:40:56  brouard
   you to do it.  More covariates you add, slower the    Summary: Still testing ilc32 on OSX
   convergence.  
     Revision 1.176  2015/01/03 16:45:04  brouard
   The advantage of this computer programme, compared to a simple    *** empty log message ***
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.175  2015/01/03 16:33:42  brouard
   intermediate interview, the information is lost, but taken into    *** empty log message ***
   account using an interpolation or extrapolation.    
     Revision 1.174  2015/01/03 16:15:49  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: Still in cross-compilation
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.173  2015/01/03 12:06:26  brouard
   states. This elementary transition (by month or quarter trimester,    Summary: trying to detect cross-compilation
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.172  2014/12/27 12:07:47  brouard
   and the contribution of each individual to the likelihood is simply    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   hPijx.  
     Revision 1.171  2014/12/23 13:26:59  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Summary: Back from Visual C
   of the life expectancies. It also computes the prevalence limits.  
      Still problem with utsname.h on Windows
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.170  2014/12/23 11:17:12  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Cleaning some \%% back to %%
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.169  2014/12/22 23:08:31  brouard
   **********************************************************************/    Summary: 0.98p
    
 #include <math.h>    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.168  2014/12/22 15:17:42  brouard
 #include <unistd.h>    Summary: update
   
 #define MAXLINE 256    Revision 1.167  2014/12/22 13:50:56  brouard
 #define GNUPLOTPROGRAM "gnuplot"    Summary: Testing uname and compiler version and if compiled 32 or 64
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Testing on Linux 64
 /*#define DEBUG*/  
 #define windows    Revision 1.166  2014/12/22 11:40:47  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    *** empty log message ***
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.165  2014/12/16 11:20:36  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: After compiling on Visual C
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     * imach.c (Module): Merging 1.61 to 1.162
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.164  2014/12/16 10:52:11  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    * imach.c (Module): Merging 1.61 to 1.162
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.163  2014/12/16 10:30:11  brouard
 #define AGEBASE 40    * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.162  2014/09/25 11:43:39  brouard
 int erreur; /* Error number */    Summary: temporary backup 0.99!
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.1  2014/09/16 11:06:58  brouard
 int npar=NPARMAX;    Summary: With some code (wrong) for nlopt
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Author:
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.160  2014/09/02 09:24:05  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    *** empty log message ***
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.159  2014/09/01 10:34:10  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Summary: WIN32
 double jmean; /* Mean space between 2 waves */    Author: Brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.158  2014/08/27 17:11:51  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    *** empty log message ***
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.157  2014/08/27 16:26:55  brouard
   char filerese[FILENAMELENGTH];    Summary: Preparing windows Visual studio version
  FILE  *ficresvij;    Author: Brouard
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    In order to compile on Visual studio, time.h is now correct and time_t
   char fileresvpl[FILENAMELENGTH];    and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
 #define NR_END 1    Trying to suppress #ifdef LINUX
 #define FREE_ARG char*    Add xdg-open for __linux in order to open default browser.
 #define FTOL 1.0e-10  
     Revision 1.156  2014/08/25 20:10:10  brouard
 #define NRANSI    *** empty log message ***
 #define ITMAX 200  
     Revision 1.155  2014/08/25 18:32:34  brouard
 #define TOL 2.0e-4    Summary: New compile, minor changes
     Author: Brouard
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.154  2014/06/20 17:32:08  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Summary: Outputs now all graphs of convergence to period prevalence
   
 #define GOLD 1.618034    Revision 1.153  2014/06/20 16:45:46  brouard
 #define GLIMIT 100.0    Summary: If 3 live state, convergence to period prevalence on same graph
 #define TINY 1.0e-20    Author: Brouard
   
 static double maxarg1,maxarg2;    Revision 1.152  2014/06/18 17:54:09  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.151  2014/06/18 16:43:30  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    *** empty log message ***
 #define rint(a) floor(a+0.5)  
     Revision 1.150  2014/06/18 16:42:35  brouard
 static double sqrarg;    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Author: brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.149  2014/06/18 15:51:14  brouard
 int imx;    Summary: Some fixes in parameter files errors
 int stepm;    Author: Nicolas Brouard
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.148  2014/06/17 17:38:48  brouard
 int estepm;    Summary: Nothing new
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Author: Brouard
   
 int m,nb;    Just a new packaging for OS/X version 0.98nS
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.147  2014/06/16 10:33:11  brouard
 double **pmmij, ***probs, ***mobaverage;    *** empty log message ***
 double dateintmean=0;  
     Revision 1.146  2014/06/16 10:20:28  brouard
 double *weight;    Summary: Merge
 int **s; /* Status */    Author: Brouard
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Merge, before building revised version.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.145  2014/06/10 21:23:15  brouard
 double ftolhess; /* Tolerance for computing hessian */    Summary: Debugging with valgrind
     Author: Nicolas Brouard
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Lot of changes in order to output the results with some covariates
 {    After the Edimburgh REVES conference 2014, it seems mandatory to
    char *s;                             /* pointer */    improve the code.
    int  l1, l2;                         /* length counters */    No more memory valgrind error but a lot has to be done in order to
     continue the work of splitting the code into subroutines.
    l1 = strlen( path );                 /* length of path */    Also, decodemodel has been improved. Tricode is still not
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    optimal. nbcode should be improved. Documentation has been added in
 #ifdef windows    the source code.
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Revision 1.143  2014/01/26 09:45:38  brouard
    s = strrchr( path, '/' );            /* find last / */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #if     defined(__bsd__)                /* get current working directory */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
       extern char       *getwd( );  
     Revision 1.142  2014/01/26 03:57:36  brouard
       if ( getwd( dirc ) == NULL ) {    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 #else  
       extern char       *getcwd( );    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.141  2014/01/26 02:42:01  brouard
 #endif    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.140  2011/09/02 10:37:54  brouard
       strcpy( name, path );             /* we've got it */    Summary: times.h is ok with mingw32 now.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.139  2010/06/14 07:50:17  brouard
       l2 = strlen( s );                 /* length of filename */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.138  2010/04/30 18:19:40  brouard
       dirc[l1-l2] = 0;                  /* add zero */    *** empty log message ***
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.137  2010/04/29 18:11:38  brouard
 #ifdef windows    (Module): Checking covariates for more complex models
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    than V1+V2. A lot of change to be done. Unstable.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.136  2010/04/26 20:30:53  brouard
 #endif    (Module): merging some libgsl code. Fixing computation
    s = strrchr( name, '.' );            /* find last / */    of likelione (using inter/intrapolation if mle = 0) in order to
    s++;    get same likelihood as if mle=1.
    strcpy(ext,s);                       /* save extension */    Some cleaning of code and comments added.
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.135  2009/10/29 15:33:14  brouard
    strncpy( finame, name, l1-l2);    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.134  2009/10/29 13:18:53  brouard
 }    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
     Revision 1.133  2009/07/06 10:21:25  brouard
 /******************************************/    just nforces
   
 void replace(char *s, char*t)    Revision 1.132  2009/07/06 08:22:05  brouard
 {    Many tings
   int i;  
   int lg=20;    Revision 1.131  2009/06/20 16:22:47  brouard
   i=0;    Some dimensions resccaled
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.130  2009/05/26 06:44:34  brouard
     (s[i] = t[i]);    (Module): Max Covariate is now set to 20 instead of 8. A
     if (t[i]== '\\') s[i]='/';    lot of cleaning with variables initialized to 0. Trying to make
   }    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 }  
     Revision 1.129  2007/08/31 13:49:27  lievre
 int nbocc(char *s, char occ)    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 {  
   int i,j=0;    Revision 1.128  2006/06/30 13:02:05  brouard
   int lg=20;    (Module): Clarifications on computing e.j
   i=0;  
   lg=strlen(s);    Revision 1.127  2006/04/28 18:11:50  brouard
   for(i=0; i<= lg; i++) {    (Module): Yes the sum of survivors was wrong since
   if  (s[i] == occ ) j++;    imach-114 because nhstepm was no more computed in the age
   }    loop. Now we define nhstepma in the age loop.
   return j;    (Module): In order to speed up (in case of numerous covariates) we
 }    compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
 void cutv(char *u,char *v, char*t, char occ)    deviation (needs data from the Hessian matrices) which slows the
 {    computation.
   int i,lg,j,p=0;    In the future we should be able to stop the program is only health
   i=0;    expectancies and graph are needed without standard deviations.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    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
   lg=strlen(t);    loop. Now we define nhstepma in the age loop.
   for(j=0; j<p; j++) {    Version 0.98h
     (u[j] = t[j]);  
   }    Revision 1.125  2006/04/04 15:20:31  lievre
      u[p]='\0';    Errors in calculation of health expectancies. Age was not initialized.
     Forecasting file added.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.124  2006/03/22 17:13:53  lievre
   }    Parameters are printed with %lf instead of %f (more numbers after the comma).
 }    The log-likelihood is printed in the log file
   
 /********************** nrerror ********************/    Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
 void nrerror(char error_text[])    name. <head> headers where missing.
 {  
   fprintf(stderr,"ERREUR ...\n");    * imach.c (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 1.122  2006/03/20 09:45:41  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    (Module): Weights can have a decimal point as for
   if (!v) nrerror("allocation failure in vector");    English (a comma might work with a correct LC_NUMERIC environment,
   return v-nl+NR_END;    otherwise the weight is truncated).
 }    Modification of warning when the covariates values are not 0 or
     1.
 /************************ free vector ******************/    Version 0.98g
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.121  2006/03/16 17:45:01  lievre
   free((FREE_ARG)(v+nl-NR_END));    * imach.c (Module): Comments concerning covariates added
 }  
     * imach.c (Module): refinements in the computation of lli if
 /************************ivector *******************************/    status=-2 in order to have more reliable computation if stepm is
 int *ivector(long nl,long nh)    not 1 month. Version 0.98f
 {  
   int *v;    Revision 1.120  2006/03/16 15:10:38  lievre
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): refinements in the computation of lli if
   if (!v) nrerror("allocation failure in ivector");    status=-2 in order to have more reliable computation if stepm is
   return v-nl+NR_END;    not 1 month. Version 0.98f
 }  
     Revision 1.119  2006/03/15 17:42:26  brouard
 /******************free ivector **************************/    (Module): Bug if status = -2, the loglikelihood was
 void free_ivector(int *v, long nl, long nh)    computed as likelihood omitting the logarithm. Version O.98e
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.118  2006/03/14 18:20:07  brouard
 }    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 /******************* imatrix *******************************/    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Module): Function pstamp added
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Module): Version 0.98d
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.117  2006/03/14 17:16:22  brouard
   int **m;    (Module): varevsij Comments added explaining the second
      table of variances if popbased=1 .
   /* allocate pointers to rows */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Module): Function pstamp added
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Version 0.98d
   m += NR_END;  
   m -= nrl;    Revision 1.116  2006/03/06 10:29:27  brouard
      (Module): Variance-covariance wrong links and
      varian-covariance of ej. is needed (Saito).
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.115  2006/02/27 12:17:45  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): One freematrix added in mlikeli! 0.98c
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.114  2006/02/26 12:57:58  brouard
      (Module): Some improvements in processing parameter
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    filename with strsep.
    
   /* return pointer to array of pointers to rows */    Revision 1.113  2006/02/24 14:20:24  brouard
   return m;    (Module): Memory leaks checks with valgrind and:
 }    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.112  2006/01/30 09:55:26  brouard
       int **m;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.111  2006/01/25 20:38:18  brouard
 {    (Module): Lots of cleaning and bugs added (Gompertz)
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    (Module): Comments can be added in data file. Missing date values
   free((FREE_ARG) (m+nrl-NR_END));    can be a simple dot '.'.
 }  
     Revision 1.110  2006/01/25 00:51:50  brouard
 /******************* matrix *******************************/    (Module): Lots of cleaning and bugs added (Gompertz)
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.109  2006/01/24 19:37:15  brouard
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    (Module): Comments (lines starting with a #) are allowed in data.
   double **m;  
     Revision 1.108  2006/01/19 18:05:42  lievre
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Gnuplot problem appeared...
   if (!m) nrerror("allocation failure 1 in matrix()");    To be fixed
   m += NR_END;  
   m -= nrl;    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.106  2006/01/19 13:24:36  brouard
   m[nrl] += NR_END;    Some cleaning and links added in html output
   m[nrl] -= ncl;  
     Revision 1.105  2006/01/05 20:23:19  lievre
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    *** empty log message ***
   return m;  
 }    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 /*************************free matrix ************************/    (Module): If the status is missing at the last wave but we know
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    that the person is alive, then we can code his/her status as -2
 {    (instead of missing=-1 in earlier versions) and his/her
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    contributions to the likelihood is 1 - Prob of dying from last
   free((FREE_ARG)(m+nrl-NR_END));    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 }    the healthy state at last known wave). Version is 0.98
   
 /******************* ma3x *******************************/    Revision 1.103  2005/09/30 15:54:49  lievre
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    (Module): sump fixed, loop imx fixed, and simplifications.
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.102  2004/09/15 17:31:30  brouard
   double ***m;    Add the possibility to read data file including tab characters.
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.101  2004/09/15 10:38:38  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    Fix on curr_time
   m += NR_END;  
   m -= nrl;    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.99  2004/06/05 08:57:40  brouard
   m[nrl] += NR_END;    *** empty log message ***
   m[nrl] -= ncl;  
     Revision 1.98  2004/05/16 15:05:56  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    state at each age, but using a Gompertz model: log u =a + b*age .
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    This is the basic analysis of mortality and should be done before any
   m[nrl][ncl] += NR_END;    other analysis, in order to test if the mortality estimated from the
   m[nrl][ncl] -= nll;    cross-longitudinal survey is different from the mortality estimated
   for (j=ncl+1; j<=nch; j++)    from other sources like vital statistic data.
     m[nrl][j]=m[nrl][j-1]+nlay;  
      The same imach parameter file can be used but the option for mle should be -3.
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Agnès, who wrote this part of the code, tried to keep most of the
     for (j=ncl+1; j<=nch; j++)    former routines in order to include the new code within the former code.
       m[i][j]=m[i][j-1]+nlay;  
   }    The output is very simple: only an estimate of the intercept and of
   return m;    the slope with 95% confident intervals.
 }  
     Current limitations:
 /*************************free ma3x ************************/    A) Even if you enter covariates, i.e. with the
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 {    B) There is no computation of Life Expectancy nor Life Table.
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.97  2004/02/20 13:25:42  lievre
   free((FREE_ARG)(m+nrl-NR_END));    Version 0.96d. Population forecasting command line is (temporarily)
 }    suppressed.
   
 /***************** f1dim *************************/    Revision 1.96  2003/07/15 15:38:55  brouard
 extern int ncom;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 extern double *pcom,*xicom;    rewritten within the same printf. Workaround: many printfs.
 extern double (*nrfunc)(double []);  
      Revision 1.95  2003/07/08 07:54:34  brouard
 double f1dim(double x)    * imach.c (Repository):
 {    (Repository): Using imachwizard code to output a more meaningful covariance
   int j;    matrix (cov(a12,c31) instead of numbers.
   double f;  
   double *xt;    Revision 1.94  2003/06/27 13:00:02  brouard
      Just cleaning
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Revision 1.93  2003/06/25 16:33:55  brouard
   f=(*nrfunc)(xt);    (Module): On windows (cygwin) function asctime_r doesn't
   free_vector(xt,1,ncom);    exist so I changed back to asctime which exists.
   return f;    (Module): Version 0.96b
 }  
     Revision 1.92  2003/06/25 16:30:45  brouard
 /*****************brent *************************/    (Module): On windows (cygwin) function asctime_r doesn't
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    exist so I changed back to asctime which exists.
 {  
   int iter;    Revision 1.91  2003/06/25 15:30:29  brouard
   double a,b,d,etemp;    * imach.c (Repository): Duplicated warning errors corrected.
   double fu,fv,fw,fx;    (Repository): Elapsed time after each iteration is now output. It
   double ftemp;    helps to forecast when convergence will be reached. Elapsed time
   double p,q,r,tol1,tol2,u,v,w,x,xm;    is stamped in powell.  We created a new html file for the graphs
   double e=0.0;    concerning matrix of covariance. It has extension -cov.htm.
    
   a=(ax < cx ? ax : cx);    Revision 1.90  2003/06/24 12:34:15  brouard
   b=(ax > cx ? ax : cx);    (Module): Some bugs corrected for windows. Also, when
   x=w=v=bx;    mle=-1 a template is output in file "or"mypar.txt with the design
   fw=fv=fx=(*f)(x);    of the covariance matrix to be input.
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    Revision 1.89  2003/06/24 12:30:52  brouard
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    (Module): Some bugs corrected for windows. Also, when
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    mle=-1 a template is output in file "or"mypar.txt with the design
     printf(".");fflush(stdout);    of the covariance matrix to be input.
 #ifdef DEBUG  
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    Revision 1.88  2003/06/23 17:54:56  brouard
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    * imach.c (Repository): 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.
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    Revision 1.87  2003/06/18 12:26:01  brouard
       *xmin=x;    Version 0.96
       return fx;  
     }    Revision 1.86  2003/06/17 20:04:08  brouard
     ftemp=fu;    (Module): Change position of html and gnuplot routines and added
     if (fabs(e) > tol1) {    routine fileappend.
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    Revision 1.85  2003/06/17 13:12:43  brouard
       p=(x-v)*q-(x-w)*r;    * imach.c (Repository): Check when date of death was earlier that
       q=2.0*(q-r);    current date of interview. It may happen when the death was just
       if (q > 0.0) p = -p;    prior to the death. In this case, dh was negative and likelihood
       q=fabs(q);    was wrong (infinity). We still send an "Error" but patch by
       etemp=e;    assuming that the date of death was just one stepm after the
       e=d;    interview.
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    (Repository): Because some people have very long ID (first column)
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    we changed int to long in num[] and we added a new lvector for
       else {    memory allocation. But we also truncated to 8 characters (left
         d=p/q;    truncation)
         u=x+d;    (Repository): No more line truncation errors.
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    Revision 1.84  2003/06/13 21:44:43  brouard
       }    * imach.c (Repository): Replace "freqsummary" at a correct
     } else {    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
     }    parcimony.
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
     fu=(*f)(u);  
     if (fu <= fx) {    Revision 1.83  2003/06/10 13:39:11  lievre
       if (u >= x) a=x; else b=x;    *** empty log message ***
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)    Revision 1.82  2003/06/05 15:57:20  brouard
         } else {    Add log in  imach.c and  fullversion number is now printed.
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  */
             v=w;  /*
             w=u;     Interpolated Markov Chain
             fv=fw;  
             fw=fu;    Short summary of the programme:
           } else if (fu <= fv || v == x || v == w) {    
             v=u;    This program computes Healthy Life Expectancies from
             fv=fu;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
           }    first survey ("cross") where individuals from different ages are
         }    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
   nrerror("Too many iterations in brent");    second wave of interviews ("longitudinal") which measure each change
   *xmin=x;    (if any) in individual health status.  Health expectancies are
   return fx;    computed from the time spent in each health state according to a
 }    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 /****************** mnbrak ***********************/    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    conditional to be observed in state i at the first wave. Therefore
             double (*func)(double))    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 {    'age' is age and 'sex' is a covariate. If you want to have a more
   double ulim,u,r,q, dum;    complex model than "constant and age", you should modify the program
   double fu;    where the markup *Covariates have to be included here again* invites
      you to do it.  More covariates you add, slower the
   *fa=(*func)(*ax);    convergence.
   *fb=(*func)(*bx);  
   if (*fb > *fa) {    The advantage of this computer programme, compared to a simple
     SHFT(dum,*ax,*bx,dum)    multinomial logistic model, is clear when the delay between waves is not
       SHFT(dum,*fb,*fa,dum)    identical for each individual. Also, if a individual missed an
       }    intermediate interview, the information is lost, but taken into
   *cx=(*bx)+GOLD*(*bx-*ax);    account using an interpolation or extrapolation.  
   *fc=(*func)(*cx);  
   while (*fb > *fc) {    hPijx is the probability to be observed in state i at age x+h
     r=(*bx-*ax)*(*fb-*fc);    conditional to the observed state i at age x. The delay 'h' can be
     q=(*bx-*cx)*(*fb-*fa);    split into an exact number (nh*stepm) of unobserved intermediate
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    states. This elementary transition (by month, quarter,
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    semester or year) is modelled as a multinomial logistic.  The hPx
     ulim=(*bx)+GLIMIT*(*cx-*bx);    matrix is simply the matrix product of nh*stepm elementary matrices
     if ((*bx-u)*(u-*cx) > 0.0) {    and the contribution of each individual to the likelihood is simply
       fu=(*func)(u);    hPijx.
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);    Also this programme outputs the covariance matrix of the parameters but also
       if (fu < *fc) {    of the life expectancies. It also computes the period (stable) prevalence. 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    
           SHFT(*fb,*fc,fu,(*func)(u))    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
           }             Institut national d'études démographiques, Paris.
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    This software have been partly granted by Euro-REVES, a concerted action
       u=ulim;    from the European Union.
       fu=(*func)(u);    It is copyrighted identically to a GNU software product, ie programme and
     } else {    software can be distributed freely for non commercial use. Latest version
       u=(*cx)+GOLD*(*cx-*bx);    can be accessed at http://euroreves.ined.fr/imach .
       fu=(*func)(u);  
     }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     SHFT(*ax,*bx,*cx,u)    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       SHFT(*fa,*fb,*fc,fu)    
       }    **********************************************************************/
 }  /*
     main
 /*************** linmin ************************/    read parameterfile
     read datafile
 int ncom;    concatwav
 double *pcom,*xicom;    freqsummary
 double (*nrfunc)(double []);    if (mle >= 1)
        mlikeli
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    print results files
 {    if mle==1 
   double brent(double ax, double bx, double cx,       computes hessian
                double (*f)(double), double tol, double *xmin);    read end of parameter file: agemin, agemax, bage, fage, estepm
   double f1dim(double x);        begin-prev-date,...
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    open gnuplot file
               double *fc, double (*func)(double));    open html file
   int j;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   double xx,xmin,bx,ax;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   double fx,fb,fa;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
        freexexit2 possible for memory heap.
   ncom=n;  
   pcom=vector(1,n);    h Pij x                         | pij_nom  ficrestpij
   xicom=vector(1,n);     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   nrfunc=func;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   for (j=1;j<=n;j++) {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
     pcom[j]=p[j];  
     xicom[j]=xi[j];         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
   ax=0.0;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   xx=1.0;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG    forecasting if prevfcast==1 prevforecast call prevalence()
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    health expectancies
 #endif    Variance-covariance of DFLE
   for (j=1;j<=n;j++) {    prevalence()
     xi[j] *= xmin;     movingaverage()
     p[j] += xi[j];    varevsij() 
   }    if popbased==1 varevsij(,popbased)
   free_vector(xicom,1,n);    total life expectancies
   free_vector(pcom,1,n);    Variance of period (stable) prevalence
 }   end
   */
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define POWELL /* Instead of NLOPT */
             double (*func)(double []))  #define POWELLDIRECT /* Directest to decide new direction instead of Powell test */
 {  
   void linmin(double p[], double xi[], int n, double *fret,  #include <math.h>
               double (*func)(double []));  #include <stdio.h>
   int i,ibig,j;  #include <stdlib.h>
   double del,t,*pt,*ptt,*xit;  #include <string.h>
   double fp,fptt;  
   double *xits;  #ifdef _WIN32
   pt=vector(1,n);  #include <io.h>
   ptt=vector(1,n);  #include <windows.h>
   xit=vector(1,n);  #include <tchar.h>
   xits=vector(1,n);  #else
   *fret=(*func)(p);  #include <unistd.h>
   for (j=1;j<=n;j++) pt[j]=p[j];  #endif
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  #include <limits.h>
     ibig=0;  #include <sys/types.h>
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #if defined(__GNUC__)
     for (i=1;i<=n;i++)  #include <sys/utsname.h> /* Doesn't work on Windows */
       printf(" %d %.12f",i, p[i]);  #endif
     printf("\n");  
     for (i=1;i<=n;i++) {  #include <sys/stat.h>
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #include <errno.h>
       fptt=(*fret);  /* extern int errno; */
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  /* #ifdef LINUX */
 #endif  /* #include <time.h> */
       printf("%d",i);fflush(stdout);  /* #include "timeval.h" */
       linmin(p,xit,n,fret,func);  /* #else */
       if (fabs(fptt-(*fret)) > del) {  /* #include <sys/time.h> */
         del=fabs(fptt-(*fret));  /* #endif */
         ibig=i;  
       }  #include <time.h>
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  #ifdef GSL
       for (j=1;j<=n;j++) {  #include <gsl/gsl_errno.h>
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #include <gsl/gsl_multimin.h>
         printf(" x(%d)=%.12e",j,xit[j]);  #endif
       }  
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  #ifdef NLOPT
       printf("\n");  #include <nlopt.h>
 #endif  typedef struct {
     }    double (* function)(double [] );
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  } myfunc_data ;
 #ifdef DEBUG  #endif
       int k[2],l;  
       k[0]=1;  /* #include <libintl.h> */
       k[1]=-1;  /* #define _(String) gettext (String) */
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
         printf(" %.12e",p[j]);  
       printf("\n");  #define GNUPLOTPROGRAM "gnuplot"
       for(l=0;l<=1;l++) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         for (j=1;j<=n;j++) {  #define FILENAMELENGTH 132
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
         }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
 #endif  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   
   #define NINTERVMAX 8
       free_vector(xit,1,n);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       free_vector(xits,1,n);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       free_vector(ptt,1,n);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       free_vector(pt,1,n);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
       return;  #define MAXN 20000
     }  #define YEARM 12. /**< Number of months per year */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define AGESUP 130
     for (j=1;j<=n;j++) {  #define AGEBASE 40
       ptt[j]=2.0*p[j]-pt[j];  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
       xit[j]=p[j]-pt[j];  #ifdef _WIN32
       pt[j]=p[j];  #define DIRSEPARATOR '\\'
     }  #define CHARSEPARATOR "\\"
     fptt=(*func)(ptt);  #define ODIRSEPARATOR '/'
     if (fptt < fp) {  #else
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define DIRSEPARATOR '/'
       if (t < 0.0) {  #define CHARSEPARATOR "/"
         linmin(p,xit,n,fret,func);  #define ODIRSEPARATOR '\\'
         for (j=1;j<=n;j++) {  #endif
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /* $Id$ */
         }  /* $State$ */
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  char version[]="Imach version 0.98p, Février 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
         for(j=1;j<=n;j++)  char fullversion[]="$Revision$ $Date$"; 
           printf(" %.12e",xit[j]);  char strstart[80];
         printf("\n");  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 #endif  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       }  int nvar=0, nforce=0; /* Number of variables, number of forces */
     }  /* 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) */
 }  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
 /**** Prevalence limit ****************/  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   int cptcovprodnoage=0; /**< Number of covariate products without age */   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int cptcoveff=0; /* Total number of covariates to vary for printing results */
 {  int cptcov=0; /* Working variable */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int npar=NPARMAX;
      matrix by transitions matrix until convergence is reached */  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
   int i, ii,j,k;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   double min, max, maxmin, maxmax,sumnew=0.;  int popbased=0;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  int *wav; /* Number of waves for this individuual 0 is possible */
   double **newm;  int maxwav=0; /* Maxim number of waves */
   double agefin, delaymax=50 ; /* Max number of years to converge */  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   for (ii=1;ii<=nlstate+ndeath;ii++)  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     for (j=1;j<=nlstate+ndeath;j++){                     to the likelihood and the sum of weights (done by funcone)*/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int mle=1, weightopt=0;
     }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    cov[1]=1.;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
               * wave mi and wave mi+1 is not an exact multiple of stepm. */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int countcallfunc=0;  /* Count the number of calls to func */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  double jmean=1; /* Mean space between 2 waves */
     newm=savm;  double **matprod2(); /* test */
     /* Covariates have to be included here again */  double **oldm, **newm, **savm; /* Working pointers to matrices */
      cov[2]=agefin;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    /*FILE *fic ; */ /* Used in readdata only */
       for (k=1; k<=cptcovn;k++) {  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  FILE *ficlog, *ficrespow;
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  int globpr=0; /* Global variable for printing or not */
       }  double fretone; /* Only one call to likelihood */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  long ipmx=0; /* Number of contributions */
       for (k=1; k<=cptcovprod;k++)  double sw; /* Sum of weights */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  FILE *ficresilk;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  FILE *ficresprobmorprev;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
     savm=oldm;  char filerese[FILENAMELENGTH];
     oldm=newm;  FILE *ficresstdeij;
     maxmax=0.;  char fileresstde[FILENAMELENGTH];
     for(j=1;j<=nlstate;j++){  FILE *ficrescveij;
       min=1.;  char filerescve[FILENAMELENGTH];
       max=0.;  FILE  *ficresvij;
       for(i=1; i<=nlstate; i++) {  char fileresv[FILENAMELENGTH];
         sumnew=0;  FILE  *ficresvpl;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  char fileresvpl[FILENAMELENGTH];
         prlim[i][j]= newm[i][j]/(1-sumnew);  char title[MAXLINE];
         max=FMAX(max,prlim[i][j]);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
         min=FMIN(min,prlim[i][j]);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       maxmin=max-min;  char command[FILENAMELENGTH];
       maxmax=FMAX(maxmax,maxmin);  int  outcmd=0;
     }  
     if(maxmax < ftolpl){  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       return prlim;  
     }  char filelog[FILENAMELENGTH]; /* Log file */
   }  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 /*************** transition probabilities ***************/  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
   double s1, s2;  /* struct timezone tzp; */
   /*double t34;*/  /* extern int gettimeofday(); */
   int i,j,j1, nc, ii, jj;  struct tm tml, *gmtime(), *localtime();
   
     for(i=1; i<= nlstate; i++){  extern time_t time();
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  struct tm start_time, end_time, curr_time, last_time, forecast_time;
         /*s2 += param[i][j][nc]*cov[nc];*/  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  struct tm tm;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  char strcurr[80], strfor[80];
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char *endptr;
     }  long lval;
     for(j=i+1; j<=nlstate+ndeath;j++){  double dval;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define NR_END 1
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  #define FREE_ARG char*
       }  #define FTOL 1.0e-10
       ps[i][j]=s2;  
     }  #define NRANSI 
   }  #define ITMAX 200 
     /*ps[3][2]=1;*/  
   #define TOL 2.0e-4 
   for(i=1; i<= nlstate; i++){  
      s1=0;  #define CGOLD 0.3819660 
     for(j=1; j<i; j++)  #define ZEPS 1.0e-10 
       s1+=exp(ps[i][j]);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  #define GOLD 1.618034 
     ps[i][i]=1./(s1+1.);  #define GLIMIT 100.0 
     for(j=1; j<i; j++)  #define TINY 1.0e-20 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  static double maxarg1,maxarg2;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   } /* end i */    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #define rint(a) floor(a+0.5)
     for(jj=1; jj<= nlstate+ndeath; jj++){  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
       ps[ii][jj]=0;  /* #define mytinydouble 1.0e-16 */
       ps[ii][ii]=1;  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
     }  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   }  /* static double dsqrarg; */
   /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   static double sqrarg;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     for(jj=1; jj<= nlstate+ndeath; jj++){  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
      printf("%lf ",ps[ii][jj]);  int agegomp= AGEGOMP;
    }  
     printf("\n ");  int imx; 
     }  int stepm=1;
     printf("\n ");printf("%lf ",cov[2]);*/  /* Stepm, step in month: minimum step interpolation*/
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  int estepm;
   goto end;*/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     return ps;  
 }  int m,nb;
   long *num;
 /**************** Product of 2 matrices ******************/  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  double **pmmij, ***probs;
 {  double *ageexmed,*agecens;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  double dateintmean=0;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  double *weight;
      before: only the contents of out is modified. The function returns  int **s; /* Status */
      a pointer to pointers identical to out */  double *agedc;
   long i, j, k;  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   for(i=nrl; i<= nrh; i++)                    * covar=matrix(0,NCOVMAX,1,n); 
     for(k=ncolol; k<=ncoloh; k++)                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  double  idx; 
         out[i][k] +=in[i][j]*b[j][k];  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Ndum; /** Freq of modality (tricode */
   return out;  int **codtab; /**< codtab=imatrix(1,100,1,10); */
 }  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *lsurv, *lpop, *tpop;
   
 /************* Higher Matrix Product ***************/  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double ftolhess; /**< Tolerance for computing hessian */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  /**************** split *************************/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step       the name of the file (name), its extension only (ext) and its first part of the name (finame)
      (typically every 2 years instead of every month which is too big).    */ 
      Model is determined by parameters x and covariates have to be    char  *ss;                            /* pointer */
      included manually here.    int   l1, l2;                         /* length counters */
   
      */    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i, j, d, h, k;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   double **out, cov[NCOVMAX];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   double **newm;      strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   /* Hstepm could be zero and should return the unit matrix */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for (i=1;i<=nlstate+ndeath;i++)      /* get current working directory */
     for (j=1;j<=nlstate+ndeath;j++){      /*    extern  char* getcwd ( char *buf , int len);*/
       oldm[i][j]=(i==j ? 1.0 : 0.0);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       po[i][j][0]=(i==j ? 1.0 : 0.0);        return( GLOCK_ERROR_GETCWD );
     }      }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      /* got dirc from getcwd*/
   for(h=1; h <=nhstepm; h++){      printf(" DIRC = %s \n",dirc);
     for(d=1; d <=hstepm; d++){    } else {                              /* strip direcotry from path */
       newm=savm;      ss++;                               /* after this, the filename */
       /* Covariates have to be included here again */      l2 = strlen( ss );                  /* length of filename */
       cov[1]=1.;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      strcpy( name, ss );         /* save file name */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       for (k=1; k<=cptcovage;k++)      dirc[l1-l2] = 0;                    /* add zero */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      printf(" DIRC2 = %s \n",dirc);
       for (k=1; k<=cptcovprod;k++)    }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    /* We add a separator at the end of dirc if not exists */
     l1 = strlen( dirc );                  /* length of directory */
     if( dirc[l1-1] != DIRSEPARATOR ){
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      dirc[l1] =  DIRSEPARATOR;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      dirc[l1+1] = 0; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      printf(" DIRC3 = %s \n",dirc);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    }
       savm=oldm;    ss = strrchr( name, '.' );            /* find last / */
       oldm=newm;    if (ss >0){
     }      ss++;
     for(i=1; i<=nlstate+ndeath; i++)      strcpy(ext,ss);                     /* save extension */
       for(j=1;j<=nlstate+ndeath;j++) {      l1= strlen( name);
         po[i][j][h]=newm[i][j];      l2= strlen(ss)+1;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      strncpy( finame, name, l1-l2);
          */      finame[l1-l2]= 0;
       }    }
   } /* end h */  
   return po;    return( 0 );                          /* we're done */
 }  }
   
   
 /*************** log-likelihood *************/  /******************************************/
 double func( double *x)  
 {  void replace_back_to_slash(char *s, char*t)
   int i, ii, j, k, mi, d, kk;  {
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    int i;
   double **out;    int lg=0;
   double sw; /* Sum of weights */    i=0;
   double lli; /* Individual log likelihood */    lg=strlen(t);
   long ipmx;    for(i=0; i<= lg; i++) {
   /*extern weight */      (s[i] = t[i]);
   /* We are differentiating ll according to initial status */      if (t[i]== '\\') s[i]='/';
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    }
   /*for(i=1;i<imx;i++)  }
     printf(" %d\n",s[4][i]);  
   */  char *trimbb(char *out, char *in)
   cov[1]=1.;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     char *s;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    s=out;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    while (*in != '\0'){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     for(mi=1; mi<= wav[i]-1; mi++){        in++;
       for (ii=1;ii<=nlstate+ndeath;ii++)      }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      *out++ = *in++;
       for(d=0; d<dh[mi][i]; d++){    }
         newm=savm;    *out='\0';
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return s;
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  char *cutl(char *blocc, char *alocc, char *in, char occ)
          {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         savm=oldm;       gives blocc="abcdef2ghi" and alocc="j".
         oldm=newm;       If occ is not found blocc is null and alocc is equal to in. Returns blocc
            */
            char *s, *t;
       } /* end mult */    t=in;s=in;
          while ((*in != occ) && (*in != '\0')){
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      *alocc++ = *in++;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    }
       ipmx +=1;    if( *in == occ){
       sw += weight[i];      *(alocc)='\0';
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      s=++in;
     } /* end of wave */    }
   } /* end of individual */   
     if (s == t) {/* occ not found */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      *(alocc-(in-s))='\0';
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      in=s;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    }
   return -l;    while ( *in != '\0'){
 }      *blocc++ = *in++;
     }
   
 /*********** Maximum Likelihood Estimation ***************/    *blocc='\0';
     return t;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  }
 {  char *cutv(char *blocc, char *alocc, char *in, char occ)
   int i,j, iter;  {
   double **xi,*delti;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   double fret;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   xi=matrix(1,npar,1,npar);       gives blocc="abcdef2ghi" and alocc="j".
   for (i=1;i<=npar;i++)       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     for (j=1;j<=npar;j++)    */
       xi[i][j]=(i==j ? 1.0 : 0.0);    char *s, *t;
   printf("Powell\n");    t=in;s=in;
   powell(p,xi,npar,ftol,&iter,&fret,func);    while (*in != '\0'){
       while( *in == occ){
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        *blocc++ = *in++;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        s=in;
       }
 }      *blocc++ = *in++;
     }
 /**** Computes Hessian and covariance matrix ***/    if (s == t) /* occ not found */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      *(blocc-(in-s))='\0';
 {    else
   double  **a,**y,*x,pd;      *(blocc-(in-s)-1)='\0';
   double **hess;    in=s;
   int i, j,jk;    while ( *in != '\0'){
   int *indx;      *alocc++ = *in++;
     }
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);    *alocc='\0';
   void lubksb(double **a, int npar, int *indx, double b[]) ;    return s;
   void ludcmp(double **a, int npar, int *indx, double *d) ;  }
   
   hess=matrix(1,npar,1,npar);  int nbocc(char *s, char occ)
   {
   printf("\nCalculation of the hessian matrix. Wait...\n");    int i,j=0;
   for (i=1;i<=npar;i++){    int lg=20;
     printf("%d",i);fflush(stdout);    i=0;
     hess[i][i]=hessii(p,ftolhess,i,delti);    lg=strlen(s);
     /*printf(" %f ",p[i]);*/    for(i=0; i<= lg; i++) {
     /*printf(" %lf ",hess[i][i]);*/    if  (s[i] == occ ) j++;
   }    }
      return j;
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  /* void cutv(char *u,char *v, char*t, char occ) */
         printf(".%d%d",i,j);fflush(stdout);  /* { */
         hess[i][j]=hessij(p,delti,i,j);  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
         hess[j][i]=hess[i][j];      /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
         /*printf(" %lf ",hess[i][j]);*/  /*      gives u="abcdef2ghi" and v="j" *\/ */
       }  /*   int i,lg,j,p=0; */
     }  /*   i=0; */
   }  /*   lg=strlen(t); */
   printf("\n");  /*   for(j=0; j<=lg-1; j++) { */
   /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /*   } */
    
   a=matrix(1,npar,1,npar);  /*   for(j=0; j<p; j++) { */
   y=matrix(1,npar,1,npar);  /*     (u[j] = t[j]); */
   x=vector(1,npar);  /*   } */
   indx=ivector(1,npar);  /*      u[p]='\0'; */
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*    for(j=0; j<= lg; j++) { */
   ludcmp(a,npar,indx,&pd);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   for (j=1;j<=npar;j++) {  /* } */
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  #ifdef _WIN32
     lubksb(a,npar,indx,x);  char * strsep(char **pp, const char *delim)
     for (i=1;i<=npar;i++){  {
       matcov[i][j]=x[i];    char *p, *q;
     }           
   }    if ((p = *pp) == NULL)
       return 0;
   printf("\n#Hessian matrix#\n");    if ((q = strpbrk (p, delim)) != NULL)
   for (i=1;i<=npar;i++) {    {
     for (j=1;j<=npar;j++) {      *pp = q + 1;
       printf("%.3e ",hess[i][j]);      *q = '\0';
     }    }
     printf("\n");    else
   }      *pp = 0;
     return p;
   /* Recompute Inverse */  }
   for (i=1;i<=npar;i++)  #endif
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);  /********************** nrerror ********************/
   
   /*  printf("\n#Hessian matrix recomputed#\n");  void nrerror(char error_text[])
   {
   for (j=1;j<=npar;j++) {    fprintf(stderr,"ERREUR ...\n");
     for (i=1;i<=npar;i++) x[i]=0;    fprintf(stderr,"%s\n",error_text);
     x[j]=1;    exit(EXIT_FAILURE);
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  /*********************** vector *******************/
       y[i][j]=x[i];  double *vector(int nl, int nh)
       printf("%.3e ",y[i][j]);  {
     }    double *v;
     printf("\n");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   }    if (!v) nrerror("allocation failure in vector");
   */    return v-nl+NR_END;
   }
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);  /************************ free vector ******************/
   free_vector(x,1,npar);  void free_vector(double*v, int nl, int nh)
   free_ivector(indx,1,npar);  {
   free_matrix(hess,1,npar,1,npar);    free((FREE_ARG)(v+nl-NR_END));
   }
   
 }  /************************ivector *******************************/
   int *ivector(long nl,long nh)
 /*************** hessian matrix ****************/  {
 double hessii( double x[], double delta, int theta, double delti[])    int *v;
 {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   int i;    if (!v) nrerror("allocation failure in ivector");
   int l=1, lmax=20;    return v-nl+NR_END;
   double k1,k2;  }
   double p2[NPARMAX+1];  
   double res;  /******************free ivector **************************/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  void free_ivector(int *v, long nl, long nh)
   double fx;  {
   int k=0,kmax=10;    free((FREE_ARG)(v+nl-NR_END));
   double l1;  }
   
   fx=func(x);  /************************lvector *******************************/
   for (i=1;i<=npar;i++) p2[i]=x[i];  long *lvector(long nl,long nh)
   for(l=0 ; l <=lmax; l++){  {
     l1=pow(10,l);    long *v;
     delts=delt;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     for(k=1 ; k <kmax; k=k+1){    if (!v) nrerror("allocation failure in ivector");
       delt = delta*(l1*k);    return v-nl+NR_END;
       p2[theta]=x[theta] +delt;  }
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;  /******************free lvector **************************/
       k2=func(p2)-fx;  void free_lvector(long *v, long nl, long nh)
       /*res= (k1-2.0*fx+k2)/delt/delt; */  {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    free((FREE_ARG)(v+nl-NR_END));
        }
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  /******************* imatrix *******************************/
 #endif  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  { 
         k=kmax;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       }    int **m; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    
         k=kmax; l=lmax*10.;    /* allocate pointers to rows */ 
       }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    if (!m) nrerror("allocation failure 1 in matrix()"); 
         delts=delt;    m += NR_END; 
       }    m -= nrl; 
     }    
   }    
   delti[theta]=delts;    /* allocate rows and set pointers to them */ 
   return res;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 }    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
 double hessij( double x[], double delti[], int thetai,int thetaj)    
 {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   int i;    
   int l=1, l1, lmax=20;    /* return pointer to array of pointers to rows */ 
   double k1,k2,k3,k4,res,fx;    return m; 
   double p2[NPARMAX+1];  } 
   int k;  
   /****************** free_imatrix *************************/
   fx=func(x);  void free_imatrix(m,nrl,nrh,ncl,nch)
   for (k=1; k<=2; k++) {        int **m;
     for (i=1;i<=npar;i++) p2[i]=x[i];        long nch,ncl,nrh,nrl; 
     p2[thetai]=x[thetai]+delti[thetai]/k;       /* free an int matrix allocated by imatrix() */ 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  { 
     k1=func(p2)-fx;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      free((FREE_ARG) (m+nrl-NR_END)); 
     p2[thetai]=x[thetai]+delti[thetai]/k;  } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  /******************* matrix *******************************/
    double **matrix(long nrl, long nrh, long ncl, long nch)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     k3=func(p2)-fx;    double **m;
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    if (!m) nrerror("allocation failure 1 in matrix()");
     k4=func(p2)-fx;    m += NR_END;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    m -= nrl;
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 #endif    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   }    m[nrl] += NR_END;
   return res;    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /************** Inverse of matrix **************/    return m;
 void ludcmp(double **a, int n, int *indx, double *d)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
 {  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   int i,imax,j,k;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   double big,dum,sum,temp;     */
   double *vv;  }
    
   vv=vector(1,n);  /*************************free matrix ************************/
   *d=1.0;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   for (i=1;i<=n;i++) {  {
     big=0.0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for (j=1;j<=n;j++)    free((FREE_ARG)(m+nrl-NR_END));
       if ((temp=fabs(a[i][j])) > big) big=temp;  }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  /******************* ma3x *******************************/
   }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (j=1;j<=n;j++) {  {
     for (i=1;i<j;i++) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       sum=a[i][j];    double ***m;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     big=0.0;    m += NR_END;
     for (i=j;i<=n;i++) {    m -= nrl;
       sum=a[i][j];  
       for (k=1;k<j;k++)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         sum -= a[i][k]*a[k][j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       a[i][j]=sum;    m[nrl] += NR_END;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    m[nrl] -= ncl;
         big=dum;  
         imax=i;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }  
     }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (j != imax) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       for (k=1;k<=n;k++) {    m[nrl][ncl] += NR_END;
         dum=a[imax][k];    m[nrl][ncl] -= nll;
         a[imax][k]=a[j][k];    for (j=ncl+1; j<=nch; j++) 
         a[j][k]=dum;      m[nrl][j]=m[nrl][j-1]+nlay;
       }    
       *d = -(*d);    for (i=nrl+1; i<=nrh; i++) {
       vv[imax]=vv[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     }      for (j=ncl+1; j<=nch; j++) 
     indx[j]=imax;        m[i][j]=m[i][j-1]+nlay;
     if (a[j][j] == 0.0) a[j][j]=TINY;    }
     if (j != n) {    return m; 
       dum=1.0/(a[j][j]);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       for (i=j+1;i<=n;i++) a[i][j] *= dum;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     }    */
   }  }
   free_vector(vv,1,n);  /* Doesn't work */  
 ;  /*************************free ma3x ************************/
 }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
 void lubksb(double **a, int n, int *indx, double b[])    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int i,ii=0,ip,j;    free((FREE_ARG)(m+nrl-NR_END));
   double sum;  }
    
   for (i=1;i<=n;i++) {  /*************** function subdirf ***********/
     ip=indx[i];  char *subdirf(char fileres[])
     sum=b[ip];  {
     b[ip]=b[i];    /* Caution optionfilefiname is hidden */
     if (ii)    strcpy(tmpout,optionfilefiname);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    strcat(tmpout,"/"); /* Add to the right */
     else if (sum) ii=i;    strcat(tmpout,fileres);
     b[i]=sum;    return tmpout;
   }  }
   for (i=n;i>=1;i--) {  
     sum=b[i];  /*************** function subdirf2 ***********/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  char *subdirf2(char fileres[], char *preop)
     b[i]=sum/a[i][i];  {
   }    
 }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 /************ Frequencies ********************/    strcat(tmpout,"/");
 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)    strcat(tmpout,preop);
 {  /* Some frequencies */    strcat(tmpout,fileres);
      return tmpout;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  }
   double ***freq; /* Frequencies */  
   double *pp;  /*************** function subdirf3 ***********/
   double pos, k2, dateintsum=0,k2cpt=0;  char *subdirf3(char fileres[], char *preop, char *preop2)
   FILE *ficresp;  {
   char fileresp[FILENAMELENGTH];    
      /* Caution optionfilefiname is hidden */
   pp=vector(1,nlstate);    strcpy(tmpout,optionfilefiname);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(tmpout,"/");
   strcpy(fileresp,"p");    strcat(tmpout,preop);
   strcat(fileresp,fileres);    strcat(tmpout,preop2);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    strcat(tmpout,fileres);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    return tmpout;
     exit(0);  }
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  char *asc_diff_time(long time_sec, char ascdiff[])
   j1=0;  {
      long sec_left, days, hours, minutes;
   j=cptcoveff;    days = (time_sec) / (60*60*24);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    sec_left = (time_sec) % (60*60*24);
      hours = (sec_left) / (60*60) ;
   for(k1=1; k1<=j;k1++){    sec_left = (sec_left) %(60*60);
     for(i1=1; i1<=ncodemax[k1];i1++){    minutes = (sec_left) /60;
       j1++;    sec_left = (sec_left) % (60);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
         scanf("%d", i);*/    return ascdiff;
       for (i=-1; i<=nlstate+ndeath; i++)    }
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)  /***************** f1dim *************************/
             freq[i][jk][m]=0;  extern int ncom; 
        extern double *pcom,*xicom;
       dateintsum=0;  extern double (*nrfunc)(double []); 
       k2cpt=0;   
       for (i=1; i<=imx; i++) {  double f1dim(double x) 
         bool=1;  { 
         if  (cptcovn>0) {    int j; 
           for (z1=1; z1<=cptcoveff; z1++)    double f;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double *xt; 
               bool=0;   
         }    xt=vector(1,ncom); 
         if (bool==1) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
           for(m=firstpass; m<=lastpass; m++){    f=(*nrfunc)(xt); 
             k2=anint[m][i]+(mint[m][i]/12.);    free_vector(xt,1,ncom); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    return f; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;  } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {  /*****************brent *************************/
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  { 
               }    int iter; 
                  double a,b,d,etemp;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    double fu=0,fv,fw,fx;
                 dateintsum=dateintsum+k2;    double ftemp=0.;
                 k2cpt++;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
               }    double e=0.0; 
             }   
           }    a=(ax < cx ? ax : cx); 
         }    b=(ax > cx ? ax : cx); 
       }    x=w=v=bx; 
            fw=fv=fx=(*f)(x); 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
       if  (cptcovn>0) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         fprintf(ficresp, "\n#********** Variable ");      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      printf(".");fflush(stdout);
         fprintf(ficresp, "**********\n#");      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUGBRENT
       for(i=1; i<=nlstate;i++)      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, " Age Prev(%d) N(%d) N",i,i);      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);
       fprintf(ficresp, "\n");      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
        #endif
       for(i=(int)agemin; i <= (int)agemax+3; i++){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         if(i==(int)agemax+3)        *xmin=x; 
           printf("Total");        return fx; 
         else      } 
           printf("Age %d", i);      ftemp=fu;
         for(jk=1; jk <=nlstate ; jk++){      if (fabs(e) > tol1) { 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        r=(x-w)*(fx-fv); 
             pp[jk] += freq[jk][m][i];        q=(x-v)*(fx-fw); 
         }        p=(x-v)*q-(x-w)*r; 
         for(jk=1; jk <=nlstate ; jk++){        q=2.0*(q-r); 
           for(m=-1, pos=0; m <=0 ; m++)        if (q > 0.0) p = -p; 
             pos += freq[jk][m][i];        q=fabs(q); 
           if(pp[jk]>=1.e-10)        etemp=e; 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        e=d; 
           else        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         }        else { 
           d=p/q; 
         for(jk=1; jk <=nlstate ; jk++){          u=x+d; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          if (u-a < tol2 || b-u < tol2) 
             pp[jk] += freq[jk][m][i];            d=SIGN(tol1,xm-x); 
         }        } 
       } else { 
         for(jk=1,pos=0; jk <=nlstate ; jk++)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           pos += pp[jk];      } 
         for(jk=1; jk <=nlstate ; jk++){      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
           if(pos>=1.e-5)      fu=(*f)(u); 
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      if (fu <= fx) { 
           else        if (u >= x) a=x; else b=x; 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        SHFT(v,w,x,u) 
           if( i <= (int) agemax){          SHFT(fv,fw,fx,fu) 
             if(pos>=1.e-5){          } else { 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            if (u < x) a=u; else b=u; 
               probs[i][jk][j1]= pp[jk]/pos;            if (fu <= fw || w == x) { 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              v=w; 
             }              w=u; 
             else              fv=fw; 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);              fw=fu; 
           }            } else if (fu <= fv || v == x || v == w) { 
         }              v=u; 
                      fv=fu; 
         for(jk=-1; jk <=nlstate+ndeath; jk++)            } 
           for(m=-1; m <=nlstate+ndeath; m++)          } 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    } 
         if(i <= (int) agemax)    nrerror("Too many iterations in brent"); 
           fprintf(ficresp,"\n");    *xmin=x; 
         printf("\n");    return fx; 
       }  } 
     }  
   }  /****************** mnbrak ***********************/
   dateintmean=dateintsum/k2cpt;  
    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   fclose(ficresp);              double (*func)(double)) 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  { 
   free_vector(pp,1,nlstate);    double ulim,u,r,q, dum;
      double fu; 
   /* End of Freq */   
 }    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
 /************ Prevalence ********************/    if (*fb > *fa) { 
 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)      SHFT(dum,*ax,*bx,dum) 
 {  /* Some frequencies */        SHFT(dum,*fb,*fa,dum) 
          } 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    *cx=(*bx)+GOLD*(*bx-*ax); 
   double ***freq; /* Frequencies */    *fc=(*func)(*cx); 
   double *pp;    while (*fb > *fc) { /* Declining fa, fb, fc */
   double pos, k2;      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
   pp=vector(1,nlstate);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
        ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
   j1=0;        fu=(*func)(u); 
    #ifdef DEBUG
   j=cptcoveff;        /* f(x)=A(x-u)**2+f(u) */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        double A, fparabu; 
          A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
   for(k1=1; k1<=j;k1++){        fparabu= *fa - A*(*ax-u)*(*ax-u);
     for(i1=1; i1<=ncodemax[k1];i1++){        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++;        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
        #endif 
       for (i=-1; i<=nlstate+ndeath; i++)        } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
         for (jk=-1; jk<=nlstate+ndeath; jk++)          fu=(*func)(u); 
           for(m=agemin; m <= agemax+3; m++)        if (fu < *fc) { 
             freq[i][jk][m]=0;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                  SHFT(*fb,*fc,fu,(*func)(u)) 
       for (i=1; i<=imx; i++) {            } 
         bool=1;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
         if  (cptcovn>0) {        u=ulim; 
           for (z1=1; z1<=cptcoveff; z1++)        fu=(*func)(u); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      } else { 
               bool=0;        u=(*cx)+GOLD*(*cx-*bx); 
         }        fu=(*func)(u); 
         if (bool==1) {      } 
           for(m=firstpass; m<=lastpass; m++){      SHFT(*ax,*bx,*cx,u) 
             k2=anint[m][i]+(mint[m][i]/12.);        SHFT(*fa,*fb,*fc,fu) 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        } 
               if(agev[m][i]==0) agev[m][i]=agemax+1;  } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {  /*************** linmin ************************/
                 if (calagedate>0)  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
                 else  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  the value of func at the returned location p . This is actually all accomplished by calling the
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  routines mnbrak and brent .*/
               }  int ncom; 
             }  double *pcom,*xicom;
           }  double (*nrfunc)(double []); 
         }   
       }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       for(i=(int)agemin; i <= (int)agemax+3; i++){  { 
         for(jk=1; jk <=nlstate ; jk++){    double brent(double ax, double bx, double cx, 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                 double (*f)(double), double tol, double *xmin); 
             pp[jk] += freq[jk][m][i];    double f1dim(double x); 
         }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         for(jk=1; jk <=nlstate ; jk++){                double *fc, double (*func)(double)); 
           for(m=-1, pos=0; m <=0 ; m++)    int j; 
             pos += freq[jk][m][i];    double xx,xmin,bx,ax; 
         }    double fx,fb,fa;
           
         for(jk=1; jk <=nlstate ; jk++){    ncom=n; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    pcom=vector(1,n); 
             pp[jk] += freq[jk][m][i];    xicom=vector(1,n); 
         }    nrfunc=func; 
            for (j=1;j<=n;j++) { 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      pcom[j]=p[j]; 
              xicom[j]=xi[j]; 
         for(jk=1; jk <=nlstate ; jk++){        } 
           if( i <= (int) agemax){    ax=0.0; 
             if(pos>=1.e-5){    xx=1.0; 
               probs[i][jk][j1]= pp[jk]/pos;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
             }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
           }  #ifdef DEBUG
         }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
            fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       }  #endif
     }    for (j=1;j<=n;j++) { 
   }      xi[j] *= xmin; 
       p[j] += xi[j]; 
      } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    free_vector(xicom,1,n); 
   free_vector(pp,1,nlstate);    free_vector(pcom,1,n); 
    } 
 }  /* End of Freq */  
   
 /************* Waves Concatenation ***************/  /*************** powell ************************/
   /*
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  Minimization of a function func of n variables. Input consists of an initial starting point
 {  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
      Death is a valid wave (if date is known).  such that failure to decrease by more than this amount on one iteration signals doneness. On
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  function value at p , and iter is the number of iterations taken. The routine linmin is used.
      and mw[mi+1][i]. dh depends on stepm.   */
      */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   int i, mi, m;  { 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    void linmin(double p[], double xi[], int n, double *fret, 
      double sum=0., jmean=0.;*/                double (*func)(double [])); 
     int i,ibig,j; 
   int j, k=0,jk, ju, jl;    double del,t,*pt,*ptt,*xit;
   double sum=0.;    double directest;
   jmin=1e+5;    double fp,fptt;
   jmax=-1;    double *xits;
   jmean=0.;    int niterf, itmp;
   for(i=1; i<=imx; i++){  
     mi=0;    pt=vector(1,n); 
     m=firstpass;    ptt=vector(1,n); 
     while(s[m][i] <= nlstate){    xit=vector(1,n); 
       if(s[m][i]>=1)    xits=vector(1,n); 
         mw[++mi][i]=m;    *fret=(*func)(p); 
       if(m >=lastpass)    for (j=1;j<=n;j++) pt[j]=p[j]; 
         break;      rcurr_time = time(NULL);  
       else    for (*iter=1;;++(*iter)) { 
         m++;      fp=(*fret); 
     }/* end while */      ibig=0; 
     if (s[m][i] > nlstate){      del=0.0; 
       mi++;     /* Death is another wave */      rlast_time=rcurr_time;
       /* if(mi==0)  never been interviewed correctly before death */      /* (void) gettimeofday(&curr_time,&tzp); */
          /* Only death is a correct wave */      rcurr_time = time(NULL);  
       mw[mi][i]=m;      curr_time = *localtime(&rcurr_time);
     }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
     wav[i]=mi;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
     if(mi==0)     for (i=1;i<=n;i++) {
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        printf(" %d %.12f",i, p[i]);
   }        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
   for(i=1; i<=imx; i++){      }
     for(mi=1; mi<wav[i];mi++){      printf("\n");
       if (stepm <=0)      fprintf(ficlog,"\n");
         dh[mi][i]=1;      fprintf(ficrespow,"\n");fflush(ficrespow);
       else{      if(*iter <=3){
         if (s[mw[mi+1][i]][i] > nlstate) {        tml = *localtime(&rcurr_time);
           if (agedc[i] < 2*AGESUP) {        strcpy(strcurr,asctime(&tml));
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        rforecast_time=rcurr_time; 
           if(j==0) j=1;  /* Survives at least one month after exam */        itmp = strlen(strcurr);
           k=k+1;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           if (j >= jmax) jmax=j;          strcurr[itmp-1]='\0';
           if (j <= jmin) jmin=j;        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           sum=sum+j;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for(niterf=10;niterf<=30;niterf+=10){
           }          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         }          forecast_time = *localtime(&rforecast_time);
         else{          strcpy(strfor,asctime(&forecast_time));
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          itmp = strlen(strfor);
           k=k+1;          if(strfor[itmp-1]=='\n')
           if (j >= jmax) jmax=j;          strfor[itmp-1]='\0';
           else if (j <= jmin)jmin=j;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
           sum=sum+j;        }
         }      }
         jk= j/stepm;      for (i=1;i<=n;i++) { 
         jl= j -jk*stepm;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         ju= j -(jk+1)*stepm;        fptt=(*fret); 
         if(jl <= -ju)  #ifdef DEBUG
           dh[mi][i]=jk;            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
         else            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           dh[mi][i]=jk+1;  #endif
         if(dh[mi][i]==0)        printf("%d",i);fflush(stdout);
           dh[mi][i]=1; /* At least one step */        fprintf(ficlog,"%d",i);fflush(ficlog);
       }        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
   }                                         because that direction will be replaced unless the gain del is small
   jmean=sum/k;                                        in comparison with the 'probable' gain, mu^2, with the last average direction.
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);                                        Unless the n directions are conjugate some gain in the determinant may be obtained
  }                                        with the new direction.
 /*********** Tricode ****************************/                                        */
 void tricode(int *Tvar, int **nbcode, int imx)          del=fabs(fptt-(*fret)); 
 {          ibig=i; 
   int Ndum[20],ij=1, k, j, i;        } 
   int cptcode=0;  #ifdef DEBUG
   cptcoveff=0;        printf("%d %.12e",i,(*fret));
          fprintf(ficlog,"%d %.12e",i,(*fret));
   for (k=0; k<19; k++) Ndum[k]=0;        for (j=1;j<=n;j++) {
   for (k=1; k<=7; k++) ncodemax[k]=0;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     for (i=1; i<=imx; i++) {        }
       ij=(int)(covar[Tvar[j]][i]);        for(j=1;j<=n;j++) {
       Ndum[ij]++;          printf(" p(%d)=%.12e",j,p[j]);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       if (ij > cptcode) cptcode=ij;        }
     }        printf("\n");
         fprintf(ficlog,"\n");
     for (i=0; i<=cptcode; i++) {  #endif
       if(Ndum[i]!=0) ncodemax[j]++;      } /* end i */
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
     ij=1;  #ifdef DEBUG
         int k[2],l;
         k[0]=1;
     for (i=1; i<=ncodemax[j]; i++) {        k[1]=-1;
       for (k=0; k<=19; k++) {        printf("Max: %.12e",(*func)(p));
         if (Ndum[k] != 0) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
           nbcode[Tvar[j]][ij]=k;        for (j=1;j<=n;j++) {
                    printf(" %.12e",p[j]);
           ij++;          fprintf(ficlog," %.12e",p[j]);
         }        }
         if (ij > ncodemax[j]) break;        printf("\n");
       }          fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
   }            for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
  for (k=0; k<19; k++) Ndum[k]=0;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
  for (i=1; i<=ncovmodel-2; i++) {          }
       ij=Tvar[i];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       Ndum[ij]++;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }        }
   #endif
  ij=1;  
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){        free_vector(xit,1,n); 
      Tvaraff[ij]=i;        free_vector(xits,1,n); 
      ij++;        free_vector(ptt,1,n); 
    }        free_vector(pt,1,n); 
  }        return; 
        } 
     cptcoveff=ij-1;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
         ptt[j]=2.0*p[j]-pt[j]; 
 /*********** Health Expectancies ****************/        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )      } 
       fptt=(*func)(ptt); /* f_3 */
 {      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   /* Health expectancies */        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
   double age, agelim, hf;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
   double ***p3mat,***varhe;        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   double **dnewm,**doldm;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
   double *xp;        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
   double **gp, **gm;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   double ***gradg, ***trgradg;  
   int theta;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line */
         t= t- del*SQR(fp-fptt);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
   xp=vector(1,npar);  #ifdef DEBUG
   dnewm=matrix(1,nlstate*2,1,npar);        printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
   doldm=matrix(1,nlstate*2,1,nlstate*2);        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
          printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   fprintf(ficreseij,"# Health expectancies\n");               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   fprintf(ficreseij,"# Age");        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   for(i=1; i<=nlstate;i++)               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     for(j=1; j<=nlstate;j++)        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        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);
   fprintf(ficreseij,"\n");  #endif
   #ifdef POWELLDIRECT
   if(estepm < stepm){        if (directest*t < 0.0) { /* Contradiction between both tests */
     printf ("Problem %d lower than %d\n",estepm, stepm);        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);
   }        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   else  hstepm=estepm;          fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);
   /* We compute the life expectancy from trapezoids spaced every estepm months        fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
    * This is mainly to measure the difference between two models: for example      } 
    * if stepm=24 months pijx are given only every 2 years and by summing them        if (directest < 0.0) { /* Then we use it for new direction */
    * we are calculating an estimate of the Life Expectancy assuming a linear  #else
    * progression inbetween and thus overestimating or underestimating according        if (t < 0.0) { /* Then we use it for new direction */
    * to the curvature of the survival function. If, for the same date, we  #endif
    * estimate the model with stepm=1 month, we can keep estepm to 24 months          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
    * to compare the new estimate of Life expectancy with the same linear          for (j=1;j<=n;j++) { 
    * hypothesis. A more precise result, taking into account a more precise            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
    * curvature will be obtained if estepm is as small as stepm. */            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
           }
   /* For example we decided to compute the life expectancy with the smallest unit */          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.  #ifdef DEBUG
      Look at hpijx to understand the reason of that which relies in memory size          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
      and note for a fixed period like estepm months */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for(j=1;j<=n;j++){
      survival function given by stepm (the optimization length). Unfortunately it            printf(" %.12e",xit[j]);
      means that if the survival funtion is printed only each two years of age and if            fprintf(ficlog," %.12e",xit[j]);
      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.          printf("\n");
   */          fprintf(ficlog,"\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  #endif
         } /* end of t negative */
   agelim=AGESUP;      } /* end if (fptt < fp)  */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    } 
     /* nhstepm age range expressed in number of stepm */  } 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  /**** Prevalence limit (stable or period prevalence)  ****************/
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     gp=matrix(0,nhstepm,1,nlstate*2);       matrix by transitions matrix until convergence is reached */
     gm=matrix(0,nhstepm,1,nlstate*2);    
     int i, ii,j,k;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double min, max, maxmin, maxmax,sumnew=0.;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    /* double **matprod2(); */ /* test */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      double **out, cov[NCOVMAX+1], **pmij();
      double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    
     for (ii=1;ii<=nlstate+ndeath;ii++)
     /* Computing Variances of health expectancies */      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      for(theta=1; theta <=npar; theta++){      }
       for(i=1; i<=npar; i++){    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    cov[1]=1.;
       }    
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       cptj=0;      newm=savm;
       for(j=1; j<= nlstate; j++){      /* Covariates have to be included here again */
         for(i=1; i<=nlstate; i++){      cov[2]=agefin;
           cptj=cptj+1;      
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      for (k=1; k<=cptcovn;k++) {
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           }        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
         }      }
       }      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
            /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
            /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
       for(i=1; i<=npar; i++)      
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
            /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       cptj=0;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       for(j=1; j<= nlstate; j++){      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
         for(i=1;i<=nlstate;i++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           cptj=cptj+1;      
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      savm=oldm;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      oldm=newm;
           }      maxmax=0.;
         }      for(j=1;j<=nlstate;j++){
       }        min=1.;
              max=0.;
            for(i=1; i<=nlstate; i++) {
           sumnew=0;
       for(j=1; j<= nlstate*2; j++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         for(h=0; h<=nhstepm-1; h++){          prlim[i][j]= newm[i][j]/(1-sumnew);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
         }          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
      }        }
            maxmin=max-min;
 /* End theta */        maxmax=FMAX(maxmax,maxmin);
       } /* j loop */
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      if(maxmax < ftolpl){
         return prlim;
      for(h=0; h<=nhstepm-1; h++)      }
       for(j=1; j<=nlstate*2;j++)    } /* age loop */
         for(theta=1; theta <=npar; theta++)    return prlim; /* should not reach here */
         trgradg[h][j][theta]=gradg[h][theta][j];  }
   
   /*************** transition probabilities ***************/ 
      for(i=1;i<=nlstate*2;i++)  
       for(j=1;j<=nlstate*2;j++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         varhe[i][j][(int)age] =0.;  {
     /* According to parameters values stored in x and the covariate's values stored in cov,
      printf("%d|",(int)age);fflush(stdout);       computes the probability to be observed in state j being in state i by appying the
     for(h=0;h<=nhstepm-1;h++){       model to the ncovmodel covariates (including constant and age).
       for(k=0;k<=nhstepm-1;k++){       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);       ncth covariate in the global vector x is given by the formula:
         for(i=1;i<=nlstate*2;i++)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           for(j=1;j<=nlstate*2;j++)       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;       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.
     }       Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
          */
     /* Computing expectancies */    double s1, lnpijopii;
     for(i=1; i<=nlstate;i++)    /*double t34;*/
       for(j=1; j<=nlstate;j++)    int i,j, nc, ii, jj;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      for(i=1; i<= nlstate; i++){
                  for(j=1; j<i;j++){
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += param[i][j][nc]*cov[nc];*/
         }            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     fprintf(ficreseij,"%3.0f",age );          }
     cptj=0;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     for(i=1; i<=nlstate;i++)  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       for(j=1; j<=nlstate;j++){        }
         cptj++;        for(j=i+1; j<=nlstate+ndeath;j++){
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       }            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     fprintf(ficreseij,"\n");            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
      /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     free_matrix(gm,0,nhstepm,1,nlstate*2);          }
     free_matrix(gp,0,nhstepm,1,nlstate*2);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        }
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
   }      for(i=1; i<= nlstate; i++){
   free_vector(xp,1,npar);        s1=0;
   free_matrix(dnewm,1,nlstate*2,1,npar);        for(j=1; j<i; j++){
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
 }        }
         for(j=i+1; j<=nlstate+ndeath; j++){
 /************ Variance ******************/          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
 {        }
   /* Variance of health expectancies */        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        ps[i][i]=1./(s1+1.);
   double **newm;        /* Computing other pijs */
   double **dnewm,**doldm;        for(j=1; j<i; j++)
   int i, j, nhstepm, hstepm, h, nstepm ;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   int k, cptcode;        for(j=i+1; j<=nlstate+ndeath; j++)
   double *xp;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   double **gp, **gm;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   double ***gradg, ***trgradg;      } /* end i */
   double ***p3mat;      
   double age,agelim, hf;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   int theta;        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");          ps[ii][ii]=1;
   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");      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   xp=vector(1,npar);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   dnewm=matrix(1,nlstate,1,npar);      /*   } */
   doldm=matrix(1,nlstate,1,nlstate);      /*   printf("\n "); */
        /* } */
   if(estepm < stepm){      /* printf("\n ");printf("%lf ",cov[2]);*/
     printf ("Problem %d lower than %d\n",estepm, stepm);      /*
   }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   else  hstepm=estepm;          goto end;*/
   /* For example we decided to compute the life expectancy with the smallest unit */      return ps;
   /* 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.  /**************** Product of 2 matrices ******************/
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   /* 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    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      means that if the survival funtion is printed only each two years of age and if       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    /* in, b, out are matrice of pointers which should have been initialized 
      results. So we changed our mind and took the option of the best precision.       before: only the contents of out is modified. The function returns
   */       a pointer to pointers identical to out */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    int i, j, k;
   agelim = AGESUP;    for(i=nrl; i<= nrh; i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for(k=ncolol; k<=ncoloh; k++){
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        out[i][k]=0.;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        for(j=ncl; j<=nch; j++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          out[i][k] +=in[i][j]*b[j][k];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      }
     gp=matrix(0,nhstepm,1,nlstate);    return out;
     gm=matrix(0,nhstepm,1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  /************* Higher Matrix Product ***************/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
       if (popbased==1) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         for(i=1; i<=nlstate;i++)       nhstepm*hstepm matrices. 
           prlim[i][i]=probs[(int)age][i][ij];       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       }       (typically every 2 years instead of every month which is too big 
         for the memory).
       for(j=1; j<= nlstate; j++){       Model is determined by parameters x and covariates have to be 
         for(h=0; h<=nhstepm; h++){       included manually here. 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];       */
         }  
       }    int i, j, d, h, k;
        double **out, cov[NCOVMAX+1];
       for(i=1; i<=npar; i++) /* Computes gradient */    double **newm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* Hstepm could be zero and should return the unit matrix */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (i=1;i<=nlstate+ndeath;i++)
        for (j=1;j<=nlstate+ndeath;j++){
       if (popbased==1) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
         for(i=1; i<=nlstate;i++)        po[i][j][0]=(i==j ? 1.0 : 0.0);
           prlim[i][i]=probs[(int)age][i][ij];      }
       }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
       for(j=1; j<= nlstate; j++){      for(d=1; d <=hstepm; d++){
         for(h=0; h<=nhstepm; h++){        newm=savm;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        /* Covariates have to be included here again */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        cov[1]=1.;
         }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       }        for (k=1; k<=cptcovn;k++) 
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for(j=1; j<= nlstate; j++)        for (k=1; k<=cptcovage;k++)
         for(h=0; h<=nhstepm; h++){          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        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]]];
     } /* End theta */  
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     for(h=0; h<=nhstepm; h++)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       for(j=1; j<=nlstate;j++)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(theta=1; theta <=npar; theta++)        savm=oldm;
           trgradg[h][j][theta]=gradg[h][theta][j];        oldm=newm;
       }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      for(i=1; i<=nlstate+ndeath; i++)
     for(i=1;i<=nlstate;i++)        for(j=1;j<=nlstate+ndeath;j++) {
       for(j=1;j<=nlstate;j++)          po[i][j][h]=newm[i][j];
         vareij[i][j][(int)age] =0.;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
     for(h=0;h<=nhstepm;h++){      /*printf("h=%d ",h);*/
       for(k=0;k<=nhstepm;k++){    } /* end h */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  /*     printf("\n H=%d \n",h); */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    return po;
         for(i=1;i<=nlstate;i++)  }
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  #ifdef NLOPT
       }    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     }    double fret;
     double *xt;
     fprintf(ficresvij,"%.0f ",age );    int j;
     for(i=1; i<=nlstate;i++)    myfunc_data *d2 = (myfunc_data *) pd;
       for(j=1; j<=nlstate;j++){  /* xt = (p1-1); */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    xt=vector(1,n); 
       }    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     free_matrix(gm,0,nhstepm,1,nlstate);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    printf("Function = %.12lf ",fret);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("\n");
   } /* End age */   free_vector(xt,1,n);
      return fret;
   free_vector(xp,1,npar);  }
   free_matrix(doldm,1,nlstate,1,npar);  #endif
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   /*************** log-likelihood *************/
 }  double func( double *x)
   {
 /************ Variance of prevlim ******************/    int i, ii, j, k, mi, d, kk;
 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)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 {    double **out;
   /* Variance of prevalence limit */    double sw; /* Sum of weights */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double lli; /* Individual log likelihood */
   double **newm;    int s1, s2;
   double **dnewm,**doldm;    double bbh, survp;
   int i, j, nhstepm, hstepm;    long ipmx;
   int k, cptcode;    /*extern weight */
   double *xp;    /* We are differentiating ll according to initial status */
   double *gp, *gm;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double **gradg, **trgradg;    /*for(i=1;i<imx;i++) 
   double age,agelim;      printf(" %d\n",s[4][i]);
   int theta;    */
      
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    ++countcallfunc;
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)    cov[1]=1.;
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   xp=vector(1,npar);    if(mle==1){
   dnewm=matrix(1,nlstate,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   doldm=matrix(1,nlstate,1,nlstate);        /* Computes the values of the ncovmodel covariates of the model
             depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   hstepm=1*YEARM; /* Every year of age */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */           to be observed in j being in i according to the model.
   agelim = AGESUP;         */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          cov[2+k]=covar[Tvar[k]][i];
     if (stepm >= YEARM) hstepm=1;        }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     gradg=matrix(1,npar,1,nlstate);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     gp=vector(1,nlstate);           has been calculated etc */
     gm=vector(1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(theta=1; theta <=npar; theta++){            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++){ /* Computes gradient */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(d=0; d<dh[mi][i]; d++){
       for(i=1;i<=nlstate;i++)            newm=savm;
         gp[i] = prlim[i][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
       for(i=1; i<=npar; i++) /* Computes gradient */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1;i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         gm[i] = prlim[i][i];            savm=oldm;
             oldm=newm;
       for(i=1;i<=nlstate;i++)          } /* end mult */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        
     } /* End theta */          /*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.
     trgradg =matrix(1,nlstate,1,npar);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
     for(j=1; j<=nlstate;j++)           * the nearest (and in case of equal distance, to the lowest) interval but now
       for(theta=1; theta <=npar; theta++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         trgradg[j][theta]=gradg[theta][j];           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
     for(i=1;i<=nlstate;i++)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       varpl[i][(int)age] =0.;           * -stepm/2 to stepm/2 .
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);           * For stepm=1 the results are the same as for previous versions of Imach.
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);           * For stepm > 1 the results are less biased than in previous versions. 
     for(i=1;i<=nlstate;i++)           */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     fprintf(ficresvpl,"%.0f ",age );          bbh=(double)bh[mi][i]/(double)stepm; 
     for(i=1; i<=nlstate;i++)          /* bias bh is positive if real duration
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));           * is higher than the multiple of stepm and negative otherwise.
     fprintf(ficresvpl,"\n");           */
     free_vector(gp,1,nlstate);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     free_vector(gm,1,nlstate);          if( s2 > nlstate){ 
     free_matrix(gradg,1,npar,1,nlstate);            /* i.e. if s2 is a death state and if the date of death is known 
     free_matrix(trgradg,1,nlstate,1,npar);               then the contribution to the likelihood is the probability to 
   } /* End age */               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
   free_vector(xp,1,npar);               minus probability to die before dh-stepm . 
   free_matrix(doldm,1,nlstate,1,npar);               In version up to 0.92 likelihood was computed
   free_matrix(dnewm,1,nlstate,1,nlstate);          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
 }          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
 /************ Variance of one-step probabilities  ******************/          (healthy, disable or death) and IMaCh was corrected; but when we
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          introduced the exact date of death then we should have modified
 {          the contribution of an exact death to the likelihood. This new
   int i, j, i1, k1, j1, z1;          contribution is smaller and very dependent of the step unit
   int k=0, cptcode;          stepm. It is no more the probability to die between last interview
   double **dnewm,**doldm;          and month of death but the probability to survive from last
   double *xp;          interview up to one month before death multiplied by the
   double *gp, *gm;          probability to die within a month. Thanks to Chris
   double **gradg, **trgradg;          Jackson for correcting this bug.  Former versions increased
   double age,agelim, cov[NCOVMAX];          mortality artificially. The bad side is that we add another loop
   int theta;          which slows down the processing. The difference can be up to 10%
   char fileresprob[FILENAMELENGTH];          lower mortality.
             */
   strcpy(fileresprob,"prob");            lli=log(out[s1][s2] - savm[s1][s2]);
   strcat(fileresprob,fileres);  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);          } else if  (s2==-2) {
   }            for (j=1,survp=0. ; j<=nlstate; j++) 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
              /*survp += out[s1][j]; */
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");            lli= log(survp);
   fprintf(ficresprob,"# Age");          }
   for(i=1; i<=nlstate;i++)          
     for(j=1; j<=(nlstate+ndeath);j++)          else if  (s2==-4) { 
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            for (j=3,survp=0. ; j<=nlstate; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
   fprintf(ficresprob,"\n");          } 
   
           else if  (s2==-5) { 
   xp=vector(1,npar);            for (j=1,survp=0. ; j<=2; j++)  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            lli= log(survp); 
            } 
   cov[1]=1;          
   j=cptcoveff;          else{
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   j1=0;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   for(k1=1; k1<=1;k1++){          } 
     for(i1=1; i1<=ncodemax[k1];i1++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     j1++;          /*if(lli ==000.0)*/
           /*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); */
     if  (cptcovn>0) {          ipmx +=1;
       fprintf(ficresprob, "\n#********** Variable ");          sw += weight[i];
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficresprob, "**********\n#");        } /* end of wave */
     }      } /* end of individual */
        }  else if(mle==2){
       for (age=bage; age<=fage; age ++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         cov[2]=age;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for (k=1; k<=cptcovn;k++) {        for(mi=1; mi<= wav[i]-1; mi++){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          for (ii=1;ii<=nlstate+ndeath;ii++)
                      for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         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(d=0; d<=dh[mi][i]; d++){
                    newm=savm;
         gradg=matrix(1,npar,1,9);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         trgradg=matrix(1,9,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            }
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(theta=1; theta <=npar; theta++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(i=1; i<=npar; i++)            savm=oldm;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);            oldm=newm;
                    } /* end mult */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        
                    s1=s[mw[mi][i]][i];
           k=0;          s2=s[mw[mi+1][i]][i];
           for(i=1; i<= (nlstate+ndeath); i++){          bbh=(double)bh[mi][i]/(double)stepm; 
             for(j=1; j<=(nlstate+ndeath);j++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
               k=k+1;          ipmx +=1;
               gp[k]=pmmij[i][j];          sw += weight[i];
             }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           }        } /* end of wave */
                } /* end of individual */
           for(i=1; i<=npar; i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
            for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           k=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
           for(i=1; i<=(nlstate+ndeath); i++){            for (j=1;j<=nlstate+ndeath;j++){
             for(j=1; j<=(nlstate+ndeath);j++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               k=k+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               gm[k]=pmmij[i][j];            }
             }          for(d=0; d<dh[mi][i]; d++){
           }            newm=savm;
                  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            for (kk=1; kk<=cptcovage;kk++) {
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(theta=1; theta <=npar; theta++)            savm=oldm;
             trgradg[j][theta]=gradg[theta][j];            oldm=newm;
                  } /* end mult */
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          s1=s[mw[mi][i]][i];
                  s2=s[mw[mi+1][i]][i];
         pmij(pmmij,cov,ncovmodel,x,nlstate);          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 */
         k=0;          ipmx +=1;
         for(i=1; i<=(nlstate+ndeath); i++){          sw += weight[i];
           for(j=1; j<=(nlstate+ndeath);j++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             k=k+1;        } /* end of wave */
             gm[k]=pmmij[i][j];      } /* end of individual */
           }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
              for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      /*printf("\n%d ",(int)age);        for(mi=1; mi<= wav[i]-1; mi++){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          for (ii=1;ii<=nlstate+ndeath;ii++)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            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);
         fprintf(ficresprob,"\n%d ",(int)age);            }
           for(d=0; d<dh[mi][i]; d++){
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)            newm=savm;
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            savm=oldm;
   }            oldm=newm;
   free_vector(xp,1,npar);          } /* end mult */
   fclose(ficresprob);        
            s1=s[mw[mi][i]][i];
 }          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
 /******************* Printing html file ***********/            lli=log(out[s1][s2] - savm[s1][s2]);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          }else{
                   int lastpass, int stepm, int weightopt, char model[],\            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \          }
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\          ipmx +=1;
                   char version[], int popforecast, int estepm ,/* \ */          sw += weight[i];
                   double jprev1, double mprev1,double anprev1, \          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   double jprev2, double mprev2,double anprev2){  /*      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]); */
   int jj1, k1, i1, cpt;        } /* end of wave */
   FILE *fichtm;      } /* end of individual */
   /*char optionfilehtm[FILENAMELENGTH];*/    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcpy(optionfilehtm,optionfile);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcat(optionfilehtm,".htm");        for(mi=1; mi<= wav[i]-1; mi++){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("Problem with %s \n",optionfilehtm), exit(0);            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);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            }
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          for(d=0; d<dh[mi][i]; d++){
 \n            newm=savm;
 Total number of observations=%d <br>\n            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            for (kk=1; kk<=cptcovage;kk++) {
 <hr  size=\"2\" color=\"#EC5E5E\">              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
  <ul><li>Parameter files<br>\n            }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n            savm=oldm;
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n            oldm=newm;
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n          } /* end mult */
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n        
  - Life expectancies by age and initial health status (estepm=%2d months):          s1=s[mw[mi][i]][i];
    <a href=\"e%s\">e%s</a> <br>\n</li>", \          s2=s[mw[mi+1][i]][i];
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n          sw += weight[i];
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n          /*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]);*/
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        } /* end of wave */
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n      } /* end of individual */
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  if(popforecast==1) fprintf(fichtm,"\n    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    return -l;
         <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);  /*************** log-likelihood *************/
 fprintf(fichtm," <li>Graphs</li><p>");  double funcone( double *x)
   {
  m=cptcoveff;    /* Same as likeli but slower because of a lot of printf and if */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
  jj1=0;    double **out;
  for(k1=1; k1<=m;k1++){    double lli; /* Individual log likelihood */
    for(i1=1; i1<=ncodemax[k1];i1++){    double llt;
        jj1++;    int s1, s2;
        if (cptcovn > 0) {    double bbh, survp;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    /*extern weight */
          for (cpt=1; cpt<=cptcoveff;cpt++)    /* We are differentiating ll according to initial status */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /*for(i=1;i<imx;i++) 
        }      printf(" %d\n",s[4][i]);
        /* Pij */    */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>    cov[1]=1.;
 <img src=\"pe%s%d1.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);      
        /* Quasi-incidences */    for(k=1; k<=nlstate; k++) ll[k]=0.;
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>  
 <img src=\"pe%s%d2.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        /* Stable prevalence in each health state */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        for(cpt=1; cpt<nlstate;cpt++){      for(mi=1; mi<= wav[i]-1; mi++){
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>        for (ii=1;ii<=nlstate+ndeath;ii++)
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for (j=1;j<=nlstate+ndeath;j++){
        }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(cpt=1; cpt<=nlstate;cpt++) {            savm[ii][j]=(ii==j ? 1.0 : 0.0);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          }
 interval) in state (%d): v%s%d%d.png <br>        for(d=0; d<dh[mi][i]; d++){
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            newm=savm;
      }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      for(cpt=1; cpt<=nlstate;cpt++) {          for (kk=1; kk<=cptcovage;kk++) {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }
      }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 health expectancies in states (1) and (2): e%s%d.png<br>                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
 fprintf(fichtm,"\n</body>");          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
    }          savm=oldm;
    }          oldm=newm;
 fclose(fichtm);        } /* end mult */
 }        
         s1=s[mw[mi][i]][i];
 /******************* Gnuplot file **************/        s2=s[mw[mi+1][i]][i];
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;         * is higher than the multiple of stepm and negative otherwise.
   int ng;         */
   strcpy(optionfilegnuplot,optionfilefiname);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   strcat(optionfilegnuplot,".gp.txt");          lli=log(out[s1][s2] - savm[s1][s2]);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        } else if  (s2==-2) {
     printf("Problem with file %s",optionfilegnuplot);          for (j=1,survp=0. ; j<=nlstate; j++) 
   }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
 #ifdef windows        }else if (mle==1){
     fprintf(ficgp,"cd \"%s\" \n",pathc);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 #endif        } else if(mle==2){
 m=pow(2,cptcoveff);          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 */
  /* 1eme*/          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   for (cpt=1; cpt<= nlstate ; cpt ++) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
    for (k1=1; k1<= m ; k1 ++) {          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
 #ifdef windows          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          /*lli=log(out[s1][s2]); */ /* Original formula */
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);        } /* End of if */
 #endif        ipmx +=1;
 #ifdef unix        sw += weight[i];
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        /*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]); */
 #endif        if(globpr){
           fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
 for (i=1; i<= nlstate ; i ++) {   %11.6f %11.6f %11.6f ", \
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            llt +=ll[k]*gipmx/gsw;
     for (i=1; i<= nlstate ; i ++) {            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficresilk," %10.6f\n", -llt);
 }        }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      } /* end of wave */
      for (i=1; i<= nlstate ; i ++) {    } /* end of individual */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 }      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    if(globpr==0){ /* First time we count the contributions and weights */
 #ifdef unix      gipmx=ipmx;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      gsw=sw;
 #endif    }
    }    return -l;
   }  }
   /*2 eme*/  
   
   for (k1=1; k1<= m ; k1 ++) {  /*************** function likelione ***********/
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);  {
        /* This routine should help understanding what is done with 
     for (i=1; i<= nlstate+1 ; i ++) {       the selection of individuals/waves and
       k=2*i;       to check the exact contribution to the likelihood.
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);       Plotting could be done.
       for (j=1; j<= nlstate+1 ; j ++) {     */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int k;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      if(*globpri !=0){ /* Just counts and sums, no printings */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      strcpy(fileresilk,"ilk"); 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      strcat(fileresilk,fileres);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for (j=1; j<= nlstate+1 ; j ++) {        printf("Problem with resultfile: %s\n", fileresilk);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         else fprintf(ficgp," \%%*lf (\%%*lf)");      }
 }        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(ficgp,"\" t\"\" w l 0,");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for (j=1; j<= nlstate+1 ; j ++) {      for(k=1; k<=nlstate; k++) 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 }      }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");    *fretone=(*funcone)(p);
     }    if(*globpri !=0){
   }      fclose(ficresilk);
        fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   /*3eme*/      fflush(fichtm); 
     } 
   for (k1=1; k1<= m ; k1 ++) {    return;
     for (cpt=1; cpt<= nlstate ; cpt ++) {  }
       k=2+nlstate*(2*cpt-2);  
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  /*********** Maximum Likelihood Estimation ***************/
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  {
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    int i,j, iter=0;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    double **xi;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    double fret;
     double fretone; /* Only one call to likelihood */
 */    /*  char filerespow[FILENAMELENGTH];*/
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);  #ifdef NLOPT
     int creturn;
       }    nlopt_opt opt;
     }    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   }    double *lb;
      double minf; /* the minimum objective value, upon return */
   /* CV preval stat */    double * p1; /* Shifted parameters from 0 instead of 1 */
     for (k1=1; k1<= m ; k1 ++) {    myfunc_data dinst, *d = &dinst;
     for (cpt=1; cpt<nlstate ; cpt ++) {  #endif
       k=3;  
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
       for (i=1; i< nlstate ; i ++)      for (j=1;j<=npar;j++)
         fprintf(ficgp,"+$%d",k+i+1);        xi[i][j]=(i==j ? 1.0 : 0.0);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
          strcpy(filerespow,"pow"); 
       l=3+(nlstate+ndeath)*cpt;    strcat(filerespow,fileres);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       for (i=1; i< nlstate ; i ++) {      printf("Problem with resultfile: %s\n", filerespow);
         l=3+(nlstate+ndeath)*cpt;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         fprintf(ficgp,"+$%d",l+i+1);    }
       }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      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");
   /* proba elementaires */  #ifdef POWELL
    for(i=1,jk=1; i <=nlstate; i++){    powell(p,xi,npar,ftol,&iter,&fret,func);
     for(k=1; k <=(nlstate+ndeath); k++){  #endif
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){  #ifdef NLOPT
          #ifdef NEWUOA
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
           jk++;  #else
           fprintf(ficgp,"\n");    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
         }  #endif
       }    lb=vector(0,npar-1);
     }    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
    }    nlopt_set_lower_bounds(opt, lb);
     nlopt_set_initial_step1(opt, 0.1);
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    
      for(jk=1; jk <=m; jk++) {    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    d->function = func;
        if (ng==2)    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    nlopt_set_min_objective(opt, myfunc, d);
        else    nlopt_set_xtol_rel(opt, ftol);
          fprintf(ficgp,"\nset title \"Probability\"\n");    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      printf("nlopt failed! %d\n",creturn); 
        i=1;    }
        for(k2=1; k2<=nlstate; k2++) {    else {
          k3=i;      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
          for(k=1; k<=(nlstate+ndeath); k++) {      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
            if (k != k2){      iter=1; /* not equal */
              if(ng==2)    }
                fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+1);    nlopt_destroy(opt);
              else  #endif
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    free_matrix(xi,1,npar,1,npar);
              ij=1;    fclose(ficrespow);
              for(j=3; j <=ncovmodel; j++) {    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                  ij++;  
                }  }
                else  
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  /**** Computes Hessian and covariance matrix ***/
              }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
              fprintf(ficgp,")/(1");  {
                  double  **a,**y,*x,pd;
              for(k1=1; k1 <=nlstate; k1++){      double **hess;
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    int i, j;
                ij=1;    int *indx;
                for(j=3; j <=ncovmodel; j++){  
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
                    ij++;    void lubksb(double **a, int npar, int *indx, double b[]) ;
                  }    void ludcmp(double **a, int npar, int *indx, double *d) ;
                  else    double gompertz(double p[]);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    hess=matrix(1,npar,1,npar);
                }  
                fprintf(ficgp,")");    printf("\nCalculation of the hessian matrix. Wait...\n");
              }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    for (i=1;i<=npar;i++){
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      printf("%d",i);fflush(stdout);
              i=i+ncovmodel;      fprintf(ficlog,"%d",i);fflush(ficlog);
            }     
          }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
        }      
      }      /*  printf(" %f ",p[i]);
    }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
    fclose(ficgp);    }
 }  /* end gnuplot */    
     for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
 /*************** Moving average **************/        if (j>i) { 
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   int i, cpt, cptcod;          hess[i][j]=hessij(p,delti,i,j,func,npar);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          
       for (i=1; i<=nlstate;i++)          hess[j][i]=hess[i][j];    
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          /*printf(" %lf ",hess[i][j]);*/
           mobaverage[(int)agedeb][i][cptcod]=0.;        }
          }
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    }
       for (i=1; i<=nlstate;i++){    printf("\n");
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficlog,"\n");
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    
         }    a=matrix(1,npar,1,npar);
       }    y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
        indx=ivector(1,npar);
 }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
 /************** Forecasting ******************/  
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      x[j]=1;
   int *popage;      lubksb(a,npar,indx,x);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      for (i=1;i<=npar;i++){ 
   double *popeffectif,*popcount;        matcov[i][j]=x[i];
   double ***p3mat;      }
   char fileresf[FILENAMELENGTH];    }
   
  agelim=AGESUP;    printf("\n#Hessian matrix#\n");
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
          fprintf(ficlog,"%.3e ",hess[i][j]);
   strcpy(fileresf,"f");      }
   strcat(fileresf,fileres);      printf("\n");
   if((ficresf=fopen(fileresf,"w"))==NULL) {      fprintf(ficlog,"\n");
     printf("Problem with forecast resultfile: %s\n", fileresf);    }
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*  printf("\n#Hessian matrix recomputed#\n");
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;      x[j]=1;
   if (stepm<=12) stepsize=1;      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   agelim=AGESUP;        y[i][j]=x[i];
          printf("%.3e ",y[i][j]);
   hstepm=1;        fprintf(ficlog,"%.3e ",y[i][j]);
   hstepm=hstepm/stepm;      }
   yp1=modf(dateintmean,&yp);      printf("\n");
   anprojmean=yp;      fprintf(ficlog,"\n");
   yp2=modf((yp1*12),&yp);    }
   mprojmean=yp;    */
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;    free_matrix(a,1,npar,1,npar);
   if(jprojmean==0) jprojmean=1;    free_matrix(y,1,npar,1,npar);
   if(mprojmean==0) jprojmean=1;    free_vector(x,1,npar);
      free_ivector(indx,1,npar);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    free_matrix(hess,1,npar,1,npar);
    
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  }
       k=k+1;  
       fprintf(ficresf,"\n#******");  /*************** hessian matrix ****************/
       for(j=1;j<=cptcoveff;j++) {  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  {
       }    int i;
       fprintf(ficresf,"******\n");    int l=1, lmax=20;
       fprintf(ficresf,"# StartingAge FinalAge");    double k1,k2;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    double p2[MAXPARM+1]; /* identical to x */
          double res;
          double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    double fx;
         fprintf(ficresf,"\n");    int k=0,kmax=10;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      double l1;
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fx=func(x);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for (i=1;i<=npar;i++) p2[i]=x[i];
           nhstepm = nhstepm/hstepm;    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
                l1=pow(10,l);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      delts=delt;
           oldm=oldms;savm=savms;      for(k=1 ; k <kmax; k=k+1){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          delt = delta*(l1*k);
                p2[theta]=x[theta] +delt;
           for (h=0; h<=nhstepm; h++){        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
             if (h==(int) (calagedate+YEARM*cpt)) {        p2[theta]=x[theta]-delt;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        k2=func(p2)-fx;
             }        /*res= (k1-2.0*fx+k2)/delt/delt; */
             for(j=1; j<=nlstate+ndeath;j++) {        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
               kk1=0.;kk2=0;        
               for(i=1; i<=nlstate;i++) {                #ifdef DEBUGHESS
                 if (mobilav==1)        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);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        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);
                 else {  #endif
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                 }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                          k=kmax;
               }        }
               if (h==(int)(calagedate+12*cpt)){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
                 fprintf(ficresf," %.3f", kk1);          k=kmax; l=lmax*10;
                                }
               }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             }          delts=delt;
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
         }    }
       }    delti[theta]=delts;
     }    return res; 
   }    
          }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   fclose(ficresf);  {
 }    int i;
 /************** Forecasting ******************/    int l=1, lmax=20;
 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){    double k1,k2,k3,k4,res,fx;
      double p2[MAXPARM+1];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int k;
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    fx=func(x);
   double *popeffectif,*popcount;    for (k=1; k<=2; k++) {
   double ***p3mat,***tabpop,***tabpopprev;      for (i=1;i<=npar;i++) p2[i]=x[i];
   char filerespop[FILENAMELENGTH];      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      k1=func(p2)-fx;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   agelim=AGESUP;      p2[thetai]=x[thetai]+delti[thetai]/k;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    
        p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   strcpy(filerespop,"pop");      k3=func(p2)-fx;
   strcat(filerespop,fileres);    
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      p2[thetai]=x[thetai]-delti[thetai]/k;
     printf("Problem with forecast resultfile: %s\n", filerespop);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }      k4=func(p2)-fx;
   printf("Computing forecasting: result on file '%s' \n", filerespop);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   if (mobilav==1) {  #endif
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
     movingaverage(agedeb, fage, ageminpar, mobaverage);    return res;
   }  }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /************** Inverse of matrix **************/
   if (stepm<=12) stepsize=1;  void ludcmp(double **a, int n, int *indx, double *d) 
    { 
   agelim=AGESUP;    int i,imax,j,k; 
      double big,dum,sum,temp; 
   hstepm=1;    double *vv; 
   hstepm=hstepm/stepm;   
      vv=vector(1,n); 
   if (popforecast==1) {    *d=1.0; 
     if((ficpop=fopen(popfile,"r"))==NULL) {    for (i=1;i<=n;i++) { 
       printf("Problem with population file : %s\n",popfile);exit(0);      big=0.0; 
     }      for (j=1;j<=n;j++) 
     popage=ivector(0,AGESUP);        if ((temp=fabs(a[i][j])) > big) big=temp; 
     popeffectif=vector(0,AGESUP);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     popcount=vector(0,AGESUP);      vv[i]=1.0/big; 
        } 
     i=1;      for (j=1;j<=n;j++) { 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      for (i=1;i<j;i++) { 
            sum=a[i][j]; 
     imx=i;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        a[i][j]=sum; 
   }      } 
       big=0.0; 
   for(cptcov=1;cptcov<=i2;cptcov++){      for (i=j;i<=n;i++) { 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        sum=a[i][j]; 
       k=k+1;        for (k=1;k<j;k++) 
       fprintf(ficrespop,"\n#******");          sum -= a[i][k]*a[k][j]; 
       for(j=1;j<=cptcoveff;j++) {        a[i][j]=sum; 
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       }          big=dum; 
       fprintf(ficrespop,"******\n");          imax=i; 
       fprintf(ficrespop,"# Age");        } 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      } 
       if (popforecast==1)  fprintf(ficrespop," [Population]");      if (j != imax) { 
              for (k=1;k<=n;k++) { 
       for (cpt=0; cpt<=0;cpt++) {          dum=a[imax][k]; 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            a[imax][k]=a[j][k]; 
                  a[j][k]=dum; 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        } 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        *d = -(*d); 
           nhstepm = nhstepm/hstepm;        vv[imax]=vv[j]; 
                } 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      indx[j]=imax; 
           oldm=oldms;savm=savms;      if (a[j][j] == 0.0) a[j][j]=TINY; 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        if (j != n) { 
                dum=1.0/(a[j][j]); 
           for (h=0; h<=nhstepm; h++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
             if (h==(int) (calagedate+YEARM*cpt)) {      } 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    } 
             }    free_vector(vv,1,n);  /* Doesn't work */
             for(j=1; j<=nlstate+ndeath;j++) {  ;
               kk1=0.;kk2=0;  } 
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)  void lubksb(double **a, int n, int *indx, double b[]) 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  { 
                 else {    int i,ii=0,ip,j; 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double sum; 
                 }   
               }    for (i=1;i<=n;i++) { 
               if (h==(int)(calagedate+12*cpt)){      ip=indx[i]; 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      sum=b[ip]; 
                   /*fprintf(ficrespop," %.3f", kk1);      b[ip]=b[i]; 
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      if (ii) 
               }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
             }      else if (sum) ii=i; 
             for(i=1; i<=nlstate;i++){      b[i]=sum; 
               kk1=0.;    } 
                 for(j=1; j<=nlstate;j++){    for (i=n;i>=1;i--) { 
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      sum=b[i]; 
                 }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      b[i]=sum/a[i][i]; 
             }    } 
   } 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  void pstamp(FILE *fichier)
           }  {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
         }  }
       }  
    /************ Frequencies ********************/
   /******/  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   {  /* Some frequencies */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      int i, m, jk, j1, bool, z1,j;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int first;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double ***freq; /* Frequencies */
           nhstepm = nhstepm/hstepm;    double *pp, **prop;
              double pos,posprop, k2, dateintsum=0,k2cpt=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char fileresp[FILENAMELENGTH];
           oldm=oldms;savm=savms;    
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      pp=vector(1,nlstate);
           for (h=0; h<=nhstepm; h++){    prop=matrix(1,nlstate,iagemin,iagemax+3);
             if (h==(int) (calagedate+YEARM*cpt)) {    strcpy(fileresp,"p");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    strcat(fileresp,fileres);
             }    if((ficresp=fopen(fileresp,"w"))==NULL) {
             for(j=1; j<=nlstate+ndeath;j++) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
               kk1=0.;kk2=0;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
               for(i=1; i<=nlstate;i++) {                    exit(0);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        }
               }    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    j1=0;
             }    
           }    j=cptcoveff;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }  
       }    first=1;
    }  
   }    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
      /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*    j1++; */
     for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
   if (popforecast==1) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     free_ivector(popage,0,AGESUP);          scanf("%d", i);*/
     free_vector(popeffectif,0,AGESUP);        for (i=-5; i<=nlstate+ndeath; i++)  
     free_vector(popcount,0,AGESUP);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   }            for(m=iagemin; m <= iagemax+3; m++)
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              freq[i][jk][m]=0;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        
   fclose(ficrespop);        for (i=1; i<=nlstate; i++)  
 }          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
 /***********************************************/        
 /**************** Main Program *****************/        dateintsum=0;
 /***********************************************/        k2cpt=0;
         for (i=1; i<=imx; i++) {
 int main(int argc, char *argv[])          bool=1;
 {          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
             for (z1=1; z1<=cptcoveff; z1++)       
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
   double agedeb, agefin,hf;                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                bool=0;
                 /* 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", 
   double fret;                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
   double **xi,tmp,delta;                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
                 /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
   double dum; /* Dummy variable */              } 
   double ***p3mat;          }
   int *indx;   
   char line[MAXLINE], linepar[MAXLINE];          if (bool==1){
   char title[MAXLINE];            for(m=firstpass; m<=lastpass; m++){
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];              k2=anint[m][i]+(mint[m][i]/12.);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];                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];
   char filerest[FILENAMELENGTH];                if (m<lastpass) {
   char fileregp[FILENAMELENGTH];                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   char popfile[FILENAMELENGTH];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                }
   int firstobs=1, lastobs=10;                
   int sdeb, sfin; /* Status at beginning and end */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   int c,  h , cpt,l;                  dateintsum=dateintsum+k2;
   int ju,jl, mi;                  k2cpt++;
   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 jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        } /* end i */
          
   double bage, fage, age, agelim, agebase;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   double ftolpl=FTOL;        pstamp(ficresp);
   double **prlim;        if  (cptcovn>0) {
   double *severity;          fprintf(ficresp, "\n#********** Variable "); 
   double ***param; /* Matrix of parameters */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double  *p;          fprintf(ficresp, "**********\n#");
   double **matcov; /* Matrix of covariance */          fprintf(ficlog, "\n#********** Variable "); 
   double ***delti3; /* Scale */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double *delti; /* Scale */          fprintf(ficlog, "**********\n#");
   double ***eij, ***vareij;        }
   double **varpl; /* Variances of prevalence limits by age */        for(i=1; i<=nlstate;i++) 
   double *epj, vepp;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double kk1, kk2;        fprintf(ficresp, "\n");
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        
          for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
   char version[80]="Imach version 0.8d, May 2002, INED-EUROREVES ";            fprintf(ficlog,"Total");
   char *alph[]={"a","a","b","c","d","e"}, str[4];          }else{
             if(first==1){
               first=0;
   char z[1]="c", occ;              printf("See log file for details...\n");
 #include <sys/time.h>            }
 #include <time.h>            fprintf(ficlog,"Age %d", i);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          }
            for(jk=1; jk <=nlstate ; jk++){
   /* long total_usecs;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   struct timeval start_time, end_time;              pp[jk] += freq[jk][m][i]; 
            }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for(jk=1; jk <=nlstate ; jk++){
   getcwd(pathcd, size);            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   printf("\n%s",version);            if(pp[jk]>=1.e-10){
   if(argc <=1){              if(first==1){
     printf("\nEnter the parameter file name: ");                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     scanf("%s",pathtot);              }
   }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   else{            }else{
     strcpy(pathtot,argv[1]);              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   /*cygwin_split_path(pathtot,path,optionfile);            }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          }
   /* cutv(path,optionfile,pathtot,'\\');*/  
           for(jk=1; jk <=nlstate ; jk++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);              pp[jk] += freq[jk][m][i];
   chdir(path);          }       
   replace(pathc,path);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
 /*-------- arguments in the command line --------*/            posprop += prop[jk][i];
           }
   strcpy(fileres,"r");          for(jk=1; jk <=nlstate ; jk++){
   strcat(fileres, optionfilefiname);            if(pos>=1.e-5){
   strcat(fileres,".txt");    /* Other files have txt extension */              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   /*---------arguments file --------*/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              if(first==1)
     printf("Problem with optionfile %s\n",optionfile);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     goto end;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }            }
             if( i <= iagemax){
   strcpy(filereso,"o");              if(pos>=1.e-5){
   strcat(filereso,fileres);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   if((ficparo=fopen(filereso,"w"))==NULL) {                /*probs[i][jk][j1]= pp[jk]/pos;*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                /*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
   /* Reads comments: lines beginning with '#' */                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          
     puts(line);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     fputs(line,ficparo);            for(m=-1; m <=nlstate+ndeath; m++)
   }              if(freq[jk][m][i] !=0 ) {
   ungetc(c,ficpar);              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   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);          if(i <= iagemax)
 while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficresp,"\n");
     ungetc(c,ficpar);          if(first==1)
     fgets(line, MAXLINE, ficpar);            printf("Others in log...\n");
     puts(line);          fprintf(ficlog,"\n");
     fputs(line,ficparo);        }
   }        /*}*/
   ungetc(c,ficpar);    }
      dateintmean=dateintsum/k2cpt; 
       
   covar=matrix(0,NCOVMAX,1,n);    fclose(ficresp);
   cptcovn=0;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   ncovmodel=2+cptcovn;    /* End of Freq */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  }
    
   /* Read guess parameters */  /************ Prevalence ********************/
   /* Reads comments: lines beginning with '#' */  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)
   while((c=getc(ficpar))=='#' && c!= EOF){  {  
     ungetc(c,ficpar);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     fgets(line, MAXLINE, ficpar);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     puts(line);       We still use firstpass and lastpass as another selection.
     fputs(line,ficparo);    */
   }   
   ungetc(c,ficpar);    int i, m, jk, j1, bool, z1,j;
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double **prop;
     for(i=1; i <=nlstate; i++)    double posprop; 
     for(j=1; j <=nlstate+ndeath-1; j++){    double  y2; /* in fractional years */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int iagemin, iagemax;
       fprintf(ficparo,"%1d%1d",i1,j1);    int first; /** to stop verbosity which is redirected to log file */
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){    iagemin= (int) agemin;
         fscanf(ficpar," %lf",&param[i][j][k]);    iagemax= (int) agemax;
         printf(" %lf",param[i][j][k]);    /*pp=vector(1,nlstate);*/
         fprintf(ficparo," %lf",param[i][j][k]);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       fscanf(ficpar,"\n");    j1=0;
       printf("\n");    
       fprintf(ficparo,"\n");    /*j=cptcoveff;*/
     }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    first=1;
     for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   p=param[1][1];      /*for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;*/
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        for (i=1; i<=nlstate; i++)  
     ungetc(c,ficpar);          for(m=iagemin; m <= iagemax+3; m++)
     fgets(line, MAXLINE, ficpar);            prop[i][m]=0.0;
     puts(line);       
     fputs(line,ficparo);        for (i=1; i<=imx; i++) { /* Each individual */
   }          bool=1;
   ungetc(c,ficpar);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                bool=0;
   for(i=1; i <=nlstate; i++){          } 
     for(j=1; j <=nlstate+ndeath-1; j++){          if (bool==1) { 
       fscanf(ficpar,"%1d%1d",&i1,&j1);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       printf("%1d%1d",i,j);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       fprintf(ficparo,"%1d%1d",i1,j1);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for(k=1; k<=ncovmodel;k++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         fscanf(ficpar,"%le",&delti3[i][j][k]);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         printf(" %le",delti3[i][j][k]);                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); 
         fprintf(ficparo," %le",delti3[i][j][k]);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       fscanf(ficpar,"\n");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       printf("\n");                  prop[s[m][i]][iagemax+3] += weight[i]; 
       fprintf(ficparo,"\n");                } 
     }              }
   }            } /* end selection of waves */
   delti=delti3[1][1];          }
          }
   /* Reads comments: lines beginning with '#' */        for(i=iagemin; i <= iagemax+3; i++){  
   while((c=getc(ficpar))=='#' && c!= EOF){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     ungetc(c,ficpar);            posprop += prop[jk][i]; 
     fgets(line, MAXLINE, ficpar);          } 
     puts(line);          
     fputs(line,ficparo);          for(jk=1; jk <=nlstate ; jk++){     
   }            if( i <=  iagemax){ 
   ungetc(c,ficpar);              if(posprop>=1.e-5){ 
                  probs[i][jk][j1]= prop[jk][i]/posprop;
   matcov=matrix(1,npar,1,npar);              } else{
   for(i=1; i <=npar; i++){                if(first==1){
     fscanf(ficpar,"%s",&str);                  first=0;
     printf("%s",str);                  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]);
     fprintf(ficparo,"%s",str);                }
     for(j=1; j <=i; j++){              }
       fscanf(ficpar," %le",&matcov[i][j]);            } 
       printf(" %.5le",matcov[i][j]);          }/* end jk */ 
       fprintf(ficparo," %.5le",matcov[i][j]);        }/* end i */ 
     }      /*} *//* end i1 */
     fscanf(ficpar,"\n");    } /* end j1 */
     printf("\n");    
     fprintf(ficparo,"\n");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   }    /*free_vector(pp,1,nlstate);*/
   for(i=1; i <=npar; i++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     for(j=i+1;j<=npar;j++)  }  /* End of prevalence */
       matcov[i][j]=matcov[j][i];  
      /************* Waves Concatenation ***************/
   printf("\n");  
   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)
   {
     /*-------- Rewriting paramater file ----------*/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      strcpy(rfileres,"r");    /* "Rparameterfile */       Death is a valid wave (if date is known).
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      strcat(rfileres,".");    /* */       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      strcat(rfileres,optionfilext);    /* Other files have txt extension */       and mw[mi+1][i]. dh depends on stepm.
     if((ficres =fopen(rfileres,"w"))==NULL) {       */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     }    int i, mi, m;
     fprintf(ficres,"#%s\n",version);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           double sum=0., jmean=0.;*/
     /*-------- data file ----------*/    int first;
     if((fic=fopen(datafile,"r"))==NULL)    {    int j, k=0,jk, ju, jl;
       printf("Problem with datafile: %s\n", datafile);goto end;    double sum=0.;
     }    first=0;
     jmin=100000;
     n= lastobs;    jmax=-1;
     severity = vector(1,maxwav);    jmean=0.;
     outcome=imatrix(1,maxwav+1,1,n);    for(i=1; i<=imx; i++){
     num=ivector(1,n);      mi=0;
     moisnais=vector(1,n);      m=firstpass;
     annais=vector(1,n);      while(s[m][i] <= nlstate){
     moisdc=vector(1,n);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     andc=vector(1,n);          mw[++mi][i]=m;
     agedc=vector(1,n);        if(m >=lastpass)
     cod=ivector(1,n);          break;
     weight=vector(1,n);        else
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          m++;
     mint=matrix(1,maxwav,1,n);      }/* end while */
     anint=matrix(1,maxwav,1,n);      if (s[m][i] > nlstate){
     s=imatrix(1,maxwav+1,1,n);        mi++;     /* Death is another wave */
     adl=imatrix(1,maxwav+1,1,n);            /* if(mi==0)  never been interviewed correctly before death */
     tab=ivector(1,NCOVMAX);           /* Only death is a correct wave */
     ncodemax=ivector(1,8);        mw[mi][i]=m;
       }
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {      wav[i]=mi;
       if ((i >= firstobs) && (i <=lastobs)) {      if(mi==0){
                nbwarn++;
         for (j=maxwav;j>=1;j--){        if(first==0){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           strcpy(line,stra);          first=1;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if(first==1){
         }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
                }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      } /* end mi==0 */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    } /* End individuals */
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1; i<=imx; i++){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          dh[mi][i]=1;
         for (j=ncovcol;j>=1;j--){        else{
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         }            if (agedc[i] < 2*AGESUP) {
         num[i]=atol(stra);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                      if(j==0) j=1;  /* Survives at least one month after exam */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              else if(j<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])); ij=ij+1;}*/                nberr++;
                 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]);
         i=i+1;                j=1; /* Temporary Dangerous patch */
       }                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("ii=%d", ij);                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);*/              }
   imx=i-1; /* Number of individuals */              k=k+1;
               if (j >= jmax){
   /* for (i=1; i<=imx; i++){                jmax=j;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                ijmax=i;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              }
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;              if (j <= jmin){
     }*/                jmin=j;
    /*  for (i=1; i<=imx; i++){                ijmin=i;
      if (s[4][i]==9)  s[4][i]=-1;              }
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/              sum=sum+j;
                /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   /* Calculation of the number of parameter from char model*/            }
   Tvar=ivector(1,15);          }
   Tprod=ivector(1,15);          else{
   Tvaraff=ivector(1,15);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   Tvard=imatrix(1,15,1,2);  /*        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]); */
   Tage=ivector(1,15);        
                k=k+1;
   if (strlen(model) >1){            if (j >= jmax) {
     j=0, j1=0, k1=1, k2=1;              jmax=j;
     j=nbocc(model,'+');              ijmax=i;
     j1=nbocc(model,'*');            }
     cptcovn=j+1;            else if (j <= jmin){
     cptcovprod=j1;              jmin=j;
                  ijmin=i;
     strcpy(modelsav,model);            }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       printf("Error. Non available option model=%s ",model);            /*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]);*/
       goto end;            if(j<0){
     }              nberr++;
                  printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for(i=(j+1); i>=1;i--){              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       cutv(stra,strb,modelsav,'+');            }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);            sum=sum+j;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          }
       /*scanf("%d",i);*/          jk= j/stepm;
       if (strchr(strb,'*')) {          jl= j -jk*stepm;
         cutv(strd,strc,strb,'*');          ju= j -(jk+1)*stepm;
         if (strcmp(strc,"age")==0) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           cptcovprod--;            if(jl==0){
           cutv(strb,stre,strd,'V');              dh[mi][i]=jk;
           Tvar[i]=atoi(stre);              bh[mi][i]=0;
           cptcovage++;            }else{ /* We want a negative bias in order to only have interpolation ie
             Tage[cptcovage]=i;                    * to avoid the price of an extra matrix product in likelihood */
             /*printf("stre=%s ", stre);*/              dh[mi][i]=jk+1;
         }              bh[mi][i]=ju;
         else if (strcmp(strd,"age")==0) {            }
           cptcovprod--;          }else{
           cutv(strb,stre,strc,'V');            if(jl <= -ju){
           Tvar[i]=atoi(stre);              dh[mi][i]=jk;
           cptcovage++;              bh[mi][i]=jl;       /* bias is positive if real duration
           Tage[cptcovage]=i;                                   * is higher than the multiple of stepm and negative otherwise.
         }                                   */
         else {            }
           cutv(strb,stre,strc,'V');            else{
           Tvar[i]=ncovcol+k1;              dh[mi][i]=jk+1;
           cutv(strb,strc,strd,'V');              bh[mi][i]=ju;
           Tprod[k1]=i;            }
           Tvard[k1][1]=atoi(strc);            if(dh[mi][i]==0){
           Tvard[k1][2]=atoi(stre);              dh[mi][i]=1; /* At least one step */
           Tvar[cptcovn+k2]=Tvard[k1][1];              bh[mi][i]=ju; /* At least one step */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           for (k=1; k<=lastobs;k++)            }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          } /* end if mle */
           k1++;        }
           k2=k2+2;      } /* end wave */
         }    }
       }    jmean=sum/k;
       else {    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);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    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);
        /*  scanf("%d",i);*/   }
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);  /*********** Tricode ****************************/
       }  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
       strcpy(modelsav,stra);    {
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
         scanf("%d",i);*/    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     }     * Boring subroutine which should only output nbcode[Tvar[j]][k]
 }     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       * nbcode[Tvar[j]][1]= 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    */
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     fclose(fic);    int modmaxcovj=0; /* Modality max of covariates j */
     int cptcode=0; /* Modality max of covariates j */
     /*  if(mle==1){*/    int modmincovj=0; /* Modality min of covariates j */
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }    cptcoveff=0; 
     /*-calculation of age at interview from date of interview and age at death -*/   
     agev=matrix(1,maxwav,1,imx);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {    /* Loop on covariates without age and products */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
          anint[m][i]=9999;      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
          s[m][i]=-1;                                 modality of this covariate Vj*/ 
        }        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;                                      * If product of Vn*Vm, still boolean *:
       }                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
     }                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     for (i=1; i<=imx; i++)  {                                        modality of the nth covariate of individual i. */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        if (ij > modmaxcovj)
       for(m=1; (m<= maxwav); m++){          modmaxcovj=ij; 
         if(s[m][i] >0){        else if (ij < modmincovj) 
           if (s[m][i] >= nlstate+1) {          modmincovj=ij; 
             if(agedc[i]>0)        if ((ij < -1) && (ij > NCOVMAX)){
               if(moisdc[i]!=99 && andc[i]!=9999)          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
                 agev[m][i]=agedc[i];          exit(1);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        }else
            else {        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
               if (andc[i]!=9999){        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
               agev[m][i]=-1;        /* 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
             }           female is 1, then modmaxcovj=1.*/
           }      }
           else if(s[m][i] !=9){ /* Should no more exist */      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      cptcode=modmaxcovj;
             if(mint[m][i]==99 || anint[m][i]==9999)      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
               agev[m][i]=1;     /*for (i=0; i<=cptcode; i++) {*/
             else if(agev[m][i] <agemin){      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
               agemin=agev[m][i];        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
             }          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
             else if(agev[m][i] >agemax){        }
               agemax=agev[m][i];        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
             }      } /* Ndum[-1] number of undefined modalities */
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           }      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
           else { /* =9 */      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
             agev[m][i]=1;         modmincovj=3; modmaxcovj = 7;
             s[m][i]=-1;         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
           }         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
         }         variables V1_1 and V1_2.
         else /*= 0 Unknown */         nbcode[Tvar[j]][ij]=k;
           agev[m][i]=1;         nbcode[Tvar[j]][1]=0;
       }         nbcode[Tvar[j]][2]=1;
             nbcode[Tvar[j]][3]=2;
     }      */
     for (i=1; i<=imx; i++)  {      ij=1; /* ij is similar to i but can jumps over null modalities */
       for(m=1; (m<= maxwav); m++){      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         if (s[m][i] > (nlstate+ndeath)) {        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           printf("Error: Wrong value in nlstate or ndeath\n");            /*recode from 0 */
           goto end;          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
         }            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
       }                                       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; */
             ij++;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          }
           if (ij > ncodemax[j]) break; 
     free_vector(severity,1,maxwav);        }  /* end of loop on */
     free_imatrix(outcome,1,maxwav+1,1,n);      } /* end of loop on modality */ 
     free_vector(moisnais,1,n);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     free_vector(annais,1,n);    
     /* free_matrix(mint,1,maxwav,1,n);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
        free_matrix(anint,1,maxwav,1,n);*/    
     free_vector(moisdc,1,n);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     free_vector(andc,1,n);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
         Ndum[ij]++; 
     wav=ivector(1,imx);   } 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);   ij=1;
       for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     /* Concatenates waves */     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);     if((Ndum[i]!=0) && (i<=ncovcol)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
       Tcode=ivector(1,100);       ij++;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     }else
       ncodemax[1]=1;         Tvaraff[ij]=0;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);   }
         ij--;
    codtab=imatrix(1,100,1,10);   cptcoveff=ij; /*Number of total covariates*/
    h=0;  
    m=pow(2,cptcoveff);  }
    
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){  /*********** Health Expectancies ****************/
        for(j=1; j <= ncodemax[k]; j++){  
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
            h++;  
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;  {
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    /* Health expectancies, no variances */
          }    int i, j, nhstepm, hstepm, h, nstepm;
        }    int nhstepma, nstepma; /* Decreasing with age */
      }    double age, agelim, hf;
    }    double ***p3mat;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    double eip;
       codtab[1][2]=1;codtab[2][2]=2; */  
    /* for(i=1; i <=m ;i++){    pstamp(ficreseij);
       for(k=1; k <=cptcovn; k++){    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    fprintf(ficreseij,"# Age");
       }    for(i=1; i<=nlstate;i++){
       printf("\n");      for(j=1; j<=nlstate;j++){
       }        fprintf(ficreseij," e%1d%1d ",i,j);
       scanf("%d",i);*/      }
          fprintf(ficreseij," e%1d. ",i);
    /* Calculates basic frequencies. Computes observed prevalence at single age    }
        and prints on file fileres'p'. */    fprintf(ficreseij,"\n");
   
        
        if(estepm < stepm){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf ("Problem %d lower than %d\n",estepm, stepm);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    else  hstepm=estepm;   
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* We compute the life expectancy from trapezoids spaced every estepm months
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     * This is mainly to measure the difference between two models: for example
           * if stepm=24 months pijx are given only every 2 years and by summing them
     /* For Powell, parameters are in a vector p[] starting at p[1]     * we are calculating an estimate of the Life Expectancy assuming a linear 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */     * progression in between and thus overestimating or underestimating according
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
     if(mle==1){     * to compare the new estimate of Life expectancy with the same linear 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);     * hypothesis. A more precise result, taking into account a more precise
     }     * curvature will be obtained if estepm is as small as stepm. */
      
     /*--------- results files --------------*/    /* For example we decided to compute the life expectancy with the smallest unit */
     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);    /* 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. 
    jk=1;       Look at hpijx to understand the reason of that which relies in memory size
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");       and note for a fixed period like estepm months */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
    for(i=1,jk=1; i <=nlstate; i++){       survival function given by stepm (the optimization length). Unfortunately it
      for(k=1; k <=(nlstate+ndeath); k++){       means that if the survival funtion is printed only each two years of age and if
        if (k != i)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
          {       results. So we changed our mind and took the option of the best precision.
            printf("%d%d ",i,k);    */
            fprintf(ficres,"%1d%1d ",i,k);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);    agelim=AGESUP;
              fprintf(ficres,"%f ",p[jk]);    /* If stepm=6 months */
              jk++;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
            }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
            printf("\n");      
            fprintf(ficres,"\n");  /* nhstepm age range expressed in number of stepm */
          }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    }    /* if (stepm >= YEARM) hstepm=1;*/
  if(mle==1){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     /* Computing hessian and covariance matrix */    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);    for (age=bage; age<=fage; age ++){ 
  }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     printf("# Scales (for hessian or gradient estimation)\n");      /* if (stepm >= YEARM) hstepm=1;*/
      for(i=1,jk=1; i <=nlstate; i++){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {      /* If stepm=6 months */
           fprintf(ficres,"%1d%1d",i,j);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           printf("%1d%1d",i,j);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           for(k=1; k<=ncovmodel;k++){      
             printf(" %.5e",delti[jk]);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
             fprintf(ficres," %.5e",delti[jk]);      
             jk++;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           }      
           printf("\n");      printf("%d|",(int)age);fflush(stdout);
           fprintf(ficres,"\n");      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         }      
       }      /* Computing expectancies */
      }      for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++)
     k=1;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     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");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");            
     for(i=1;i<=npar;i++){            /* 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 (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;          }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/      fprintf(ficreseij,"%3.0f",age );
       fprintf(ficres,"%3d",i);      for(i=1; i<=nlstate;i++){
       printf("%3d",i);        eip=0;
       for(j=1; j<=i;j++){        for(j=1; j<=nlstate;j++){
         fprintf(ficres," %.5e",matcov[i][j]);          eip +=eij[i][j][(int)age];
         printf(" %.5e",matcov[i][j]);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
       }        }
       fprintf(ficres,"\n");        fprintf(ficreseij,"%9.4f", eip );
       printf("\n");      }
       k++;      fprintf(ficreseij,"\n");
     }      
        }
     while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       ungetc(c,ficpar);    printf("\n");
       fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"\n");
       puts(line);    
       fputs(line,ficparo);  }
     }  
     ungetc(c,ficpar);  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[] )
     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;    /* Covariances of health expectancies eij and of total life expectancies according
     if (fage <= 2) {     to initial status i, ei. .
       bage = ageminpar;    */
       fage = agemaxpar;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     }    int nhstepma, nstepma; /* Decreasing with age */
        double age, agelim, hf;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    double ***p3matp, ***p3matm, ***varhe;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    double **dnewm,**doldm;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    double *xp, *xm;
      double **gp, **gm;
     while((c=getc(ficpar))=='#' && c!= EOF){    double ***gradg, ***trgradg;
     ungetc(c,ficpar);    int theta;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    double eip, vip;
     fputs(line,ficparo);  
   }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   ungetc(c,ficpar);    xp=vector(1,npar);
      xm=vector(1,npar);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
          pstamp(ficresstdeij);
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     ungetc(c,ficpar);    fprintf(ficresstdeij,"# Age");
     fgets(line, MAXLINE, ficpar);    for(i=1; i<=nlstate;i++){
     puts(line);      for(j=1; j<=nlstate;j++)
     fputs(line,ficparo);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   }      fprintf(ficresstdeij," e%1d. ",i);
   ungetc(c,ficpar);    }
      fprintf(ficresstdeij,"\n");
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    pstamp(ficrescveij);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
   fscanf(ficpar,"pop_based=%d\n",&popbased);    for(i=1; i<=nlstate;i++)
   fprintf(ficparo,"pop_based=%d\n",popbased);        for(j=1; j<=nlstate;j++){
   fprintf(ficres,"pop_based=%d\n",popbased);          cptj= (j-1)*nlstate+i;
          for(i2=1; i2<=nlstate;i2++)
   while((c=getc(ficpar))=='#' && c!= EOF){          for(j2=1; j2<=nlstate;j2++){
     ungetc(c,ficpar);            cptj2= (j2-1)*nlstate+i2;
     fgets(line, MAXLINE, ficpar);            if(cptj2 <= cptj)
     puts(line);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     fputs(line,ficparo);          }
   }      }
   ungetc(c,ficpar);    fprintf(ficrescveij,"\n");
     
   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);    if(estepm < stepm){
 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);      printf ("Problem %d lower than %d\n",estepm, stepm);
 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);    }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
 while((c=getc(ficpar))=='#' && c!= EOF){     * This is mainly to measure the difference between two models: for example
     ungetc(c,ficpar);     * if stepm=24 months pijx are given only every 2 years and by summing them
     fgets(line, MAXLINE, ficpar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     puts(line);     * progression in between and thus overestimating or underestimating according
     fputs(line,ficparo);     * to the curvature of the survival function. If, for the same date, we 
   }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   ungetc(c,ficpar);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);     * curvature will be obtained if estepm is as small as stepm. */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    /* For 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. 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
 /*------------ gnuplot -------------*/       Look at hpijx to understand the reason of that which relies in memory size
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);       and note for a fixed period like estepm months */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 /*------------ free_vector  -------------*/       survival function given by stepm (the optimization length). Unfortunately it
  chdir(path);       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 
  free_ivector(wav,1,imx);       results. So we changed our mind and took the option of the best precision.
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);    /* If stepm=6 months */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    /* nhstepm age range expressed in number of stepm */
  fclose(ficparo);    agelim=AGESUP;
  fclose(ficres);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 /*--------- index.htm --------*/    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*--------------- Prevalence limit --------------*/    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   strcpy(filerespl,"pl");    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   strcat(filerespl,fileres);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    for (age=bage; age<=fage; age ++){ 
   }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fprintf(ficrespl,"#Prevalence limit\n");      /* if (stepm >= YEARM) hstepm=1;*/
   fprintf(ficrespl,"#Age ");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");      /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepma matrices, stored
   prlim=matrix(1,nlstate,1,nlstate);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* Computing  Variances of health expectancies */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   k=0;         decrease memory allocation */
   agebase=ageminpar;      for(theta=1; theta <=npar; theta++){
   agelim=agemaxpar;        for(i=1; i<=npar; i++){ 
   ftolpl=1.e-10;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   i1=cptcoveff;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
   if (cptcovn < 1){i1=1;}        }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   for(cptcov=1;cptcov<=i1;cptcov++){        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
         k=k+1;        for(j=1; j<= nlstate; j++){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          for(i=1; i<=nlstate; i++){
         fprintf(ficrespl,"\n#******");            for(h=0; h<=nhstepm-1; h++){
         for(j=1;j<=cptcoveff;j++)              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
         fprintf(ficrespl,"******\n");            }
                  }
         for (age=agebase; age<=agelim; age++){        }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       
           fprintf(ficrespl,"%.0f",age );        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(i=1; i<=nlstate;i++)          for(h=0; h<=nhstepm-1; h++){
           fprintf(ficrespl," %.5f", prlim[i][i]);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           fprintf(ficrespl,"\n");          }
         }      }/* End theta */
       }      
     }      
   fclose(ficrespl);      for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
   /*------------- h Pij x at various ages ------------*/          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       for(ij=1;ij<=nlstate*nlstate;ij++)
   }        for(ji=1;ji<=nlstate*nlstate;ji++)
   printf("Computing pij: result on file '%s' \n", filerespij);          varhe[ij][ji][(int)age] =0.;
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;       printf("%d|",(int)age);fflush(stdout);
   /*if (stepm<=24) stepsize=2;*/       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
   agelim=AGESUP;        for(k=0;k<=nhstepm-1;k++){
   hstepm=stepsize*YEARM; /* Every year of age */          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
            for(ij=1;ij<=nlstate*nlstate;ij++)
   k=0;            for(ji=1;ji<=nlstate*nlstate;ji++)
   for(cptcov=1;cptcov<=i1;cptcov++){              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
       k=k+1;      }
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)      /* Computing expectancies */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         fprintf(ficrespij,"******\n");      for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /* 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]);*/
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)      fprintf(ficresstdeij,"%3.0f",age );
             for(j=1; j<=nlstate+ndeath;j++)      for(i=1; i<=nlstate;i++){
               fprintf(ficrespij," %1d-%1d",i,j);        eip=0.;
           fprintf(ficrespij,"\n");        vip=0.;
            for (h=0; h<=nhstepm; h++){        for(j=1; j<=nlstate;j++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          eip += eij[i][j][(int)age];
             for(i=1; i<=nlstate;i++)          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
               for(j=1; j<=nlstate+ndeath;j++)            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
             fprintf(ficrespij,"\n");        }
              }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
           fprintf(ficrespij,"\n");      fprintf(ficresstdeij,"\n");
         }  
     }      fprintf(ficrescveij,"%3.0f",age );
   }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
   fclose(ficrespij);            for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
   /*---------- Forecasting ------------------*/                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   if((stepm == 1) && (strcmp(model,".")==0)){            }
     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(ficrescveij,"\n");
   }     
   else{    }
     erreur=108;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);    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);
   /*---------- Health expectancies and variances ------------*/    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
   strcpy(filerest,"t");    fprintf(ficlog,"\n");
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {    free_vector(xm,1,npar);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    free_vector(xp,1,npar);
   }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   strcpy(filerese,"e");  
   strcat(filerese,fileres);  /************ Variance ******************/
   if((ficreseij=fopen(filerese,"w"))==NULL) {  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  {
   }    /* Variance of health expectancies */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
  strcpy(fileresv,"v");    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
   strcat(fileresv,fileres);    
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    int movingaverage();
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    double **dnewm,**doldm;
   }    double **dnewmp,**doldmp;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    int i, j, nhstepm, hstepm, h, nstepm ;
   calagedate=-1;    int k;
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double *xp;
     double **gp, **gm;  /* for var eij */
   k=0;    double ***gradg, ***trgradg; /*for var eij */
   for(cptcov=1;cptcov<=i1;cptcov++){    double **gradgp, **trgradgp; /* for var p point j */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double *gpp, *gmp; /* for var p point j */
       k=k+1;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       fprintf(ficrest,"\n#****** ");    double ***p3mat;
       for(j=1;j<=cptcoveff;j++)    double age,agelim, hf;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***mobaverage;
       fprintf(ficrest,"******\n");    int theta;
     char digit[4];
       fprintf(ficreseij,"\n#****** ");    char digitp[25];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    char fileresprobmorprev[FILENAMELENGTH];
       fprintf(ficreseij,"******\n");  
     if(popbased==1){
       fprintf(ficresvij,"\n#****** ");      if(mobilav!=0)
       for(j=1;j<=cptcoveff;j++)        strcpy(digitp,"-populbased-mobilav-");
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      else strcpy(digitp,"-populbased-nomobil-");
       fprintf(ficresvij,"******\n");    }
     else 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      strcpy(digitp,"-stablbased-");
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      if (mobilav!=0) {
        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       oldm=oldms;savm=savms;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
     }
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    strcpy(fileresprobmorprev,"prmorprev"); 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    sprintf(digit,"%-d",ij);
       fprintf(ficrest,"\n");    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
       epj=vector(1,nlstate+1);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       for(age=bage; age <=fage ;age++){    strcat(fileresprobmorprev,fileres);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         if (popbased==1) {      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
             prlim[i][i]=probs[(int)age][i][k];    }
         }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           
         fprintf(ficrest," %4.0f",age);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    pstamp(ficresprobmorprev);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    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);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           }      fprintf(ficresprobmorprev," p.%-d SE",j);
           epj[nlstate+1] +=epj[j];      for(i=1; i<=nlstate;i++)
         }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficresprobmorprev,"\n");
           for(j=1;j <=nlstate;j++)    fprintf(ficgp,"\n# Routine varevsij");
             vepp += vareij[i][j][(int)age];    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
         for(j=1;j <=nlstate;j++){    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  /*   } */
         }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficrest,"\n");    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);
 free_matrix(mint,1,maxwav,1,n);    else
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     free_vector(weight,1,n);    fprintf(ficresvij,"# Age");
   fclose(ficreseij);    for(i=1; i<=nlstate;i++)
   fclose(ficresvij);      for(j=1; j<=nlstate;j++)
   fclose(ficrest);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   fclose(ficpar);    fprintf(ficresvij,"\n");
   free_vector(epj,1,nlstate+1);  
      xp=vector(1,npar);
   /*------- Variance limit prevalence------*/      dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   strcpy(fileresvpl,"vpl");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   strcat(fileresvpl,fileres);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     exit(0);    gpp=vector(nlstate+1,nlstate+ndeath);
   }    gmp=vector(nlstate+1,nlstate+ndeath);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   k=0;    if(estepm < stepm){
   for(cptcov=1;cptcov<=i1;cptcov++){      printf ("Problem %d lower than %d\n",estepm, stepm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;    else  hstepm=estepm;   
       fprintf(ficresvpl,"\n#****** ");    /* For example we decided to compute the life expectancy with the smallest unit */
       for(j=1;j<=cptcoveff;j++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficresvpl,"******\n");       nstepm is the number of stepm from age to agelin. 
             Look at function hpijx to understand why (it is linked to memory size questions) */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       oldm=oldms;savm=savms;       survival function given by stepm (the optimization length). Unfortunately it
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       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.
     */
   fclose(ficresvpl);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   /*---------- End : free ----------------*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      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 */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
   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);      for(theta=1; theta <=npar; theta++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   free_matrix(matcov,1,npar,1,npar);        }
   free_vector(delti,1,npar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   free_matrix(agev,1,maxwav,1,imx);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
         if (popbased==1) {
   if(erreur >0)          if(mobilav ==0){
     printf("End of Imach with error or warning %d\n",erreur);            for(i=1; i<=nlstate;i++)
   else   printf("End of Imach\n");              prlim[i][i]=probs[(int)age][i][ij];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   /* 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);*/              prlim[i][i]=mobaverage[(int)age][i][ij];
   /*printf("Total time was %d uSec.\n", total_usecs);*/          }
   /*------ End -----------*/        }
     
         for(j=1; j<= nlstate; j++){
  end:          for(h=0; h<=nhstepm; h++){
 #ifdef windows            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   /* chdir(pathcd);*/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 #endif          }
  /*system("wgnuplot graph.plt");*/        }
  /*system("../gp37mgw/wgnuplot graph.plt");*/        /* This for computing probability of death (h=1 means
  /*system("cd ../gp37mgw");*/           computed over hstepm matrices product = hstepm*stepm months) 
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/           as a weighted average of prlim.
  strcpy(plotcmd,GNUPLOTPROGRAM);        */
  strcat(plotcmd," ");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
  strcat(plotcmd,optionfilegnuplot);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
  system(plotcmd);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
 #ifdef windows        /* end probability of death */
   while (z[0] != 'q') {  
     /* chdir(path); */        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     scanf("%s",z);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     if (z[0] == 'c') system("./imach");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     else if (z[0] == 'e') system(optionfilehtm);   
     else if (z[0] == 'g') system(plotcmd);        if (popbased==1) {
     else if (z[0] == 'q') exit(0);          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
 #endif              prlim[i][i]=probs[(int)age][i][ij];
 }          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
   
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         /*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
           k=k+1; 
       /* for (k=1; k <= (int) pow(2,cptcoveff); k++){*/
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
               fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         /*}*/
       }
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.43  
changed lines
  Added in v.1.182


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