Diff for /imach/src/imach.c between versions 1.45 and 1.193

version 1.45, 2002/05/24 16:34:18 version 1.193, 2015/08/04 07:17:42
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.193  2015/08/04 07:17:42  brouard
      Summary: 0.98q4
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.192  2015/07/16 16:49:02  brouard
   first survey ("cross") where individuals from different ages are    Summary: Fixing some outputs
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.191  2015/07/14 10:00:33  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: Some fixes
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.190  2015/05/05 08:51:13  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: Adding digits in output parameters (7 digits instead of 6)
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Fix 1+age+.
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.189  2015/04/30 14:45:16  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: 0.98q2
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.188  2015/04/30 08:27:53  brouard
   where the markup *Covariates have to be included here again* invites    *** empty log message ***
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.187  2015/04/29 09:11:15  brouard
     *** empty log message ***
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.186  2015/04/23 12:01:52  brouard
   identical for each individual. Also, if a individual missed an    Summary: V1*age is working now, version 0.98q1
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Some codes had been disabled in order to simplify and Vn*age was
     working in the optimization phase, ie, giving correct MLE parameters,
   hPijx is the probability to be observed in state i at age x+h    but, as usual, outputs were not correct and program core dumped.
   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 1.185  2015/03/11 13:26:42  brouard
   states. This elementary transition (by month or quarter trimester,    Summary: Inclusion of compile and links command line for Intel Compiler
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.184  2015/03/11 11:52:39  brouard
   and the contribution of each individual to the likelihood is simply    Summary: Back from Windows 8. Intel Compiler
   hPijx.  
     Revision 1.183  2015/03/10 20:34:32  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Summary: 0.98q0, trying with directest, mnbrak fixed
   of the life expectancies. It also computes the prevalence limits.  
      We use directest instead of original Powell test; probably no
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    incidence on the results, but better justifications;
            Institut national d'études démographiques, Paris.    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   This software have been partly granted by Euro-REVES, a concerted action    wrong results.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.182  2015/02/12 08:19:57  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: Trying to keep directest which seems simpler and more general
   can be accessed at http://euroreves.ined.fr/imach .    Author: Nicolas Brouard
   **********************************************************************/  
      Revision 1.181  2015/02/11 23:22:24  brouard
 #include <math.h>    Summary: Comments on Powell added
 #include <stdio.h>  
 #include <stdlib.h>    Author:
 #include <unistd.h>  
     Revision 1.180  2015/02/11 17:33:45  brouard
 #define MAXLINE 256    Summary: Finishing move from main to function (hpijx and prevalence_limit)
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.179  2015/01/04 09:57:06  brouard
 #define FILENAMELENGTH 80    Summary: back to OS/X
 /*#define DEBUG*/  
 #define windows    Revision 1.178  2015/01/04 09:35:48  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    *** empty log message ***
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.177  2015/01/03 18:40:56  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: Still testing ilc32 on OSX
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.176  2015/01/03 16:45:04  brouard
 #define NINTERVMAX 8    *** empty log message ***
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.175  2015/01/03 16:33:42  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    *** empty log message ***
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.174  2015/01/03 16:15:49  brouard
 #define AGESUP 130    Summary: Still in cross-compilation
 #define AGEBASE 40  
     Revision 1.173  2015/01/03 12:06:26  brouard
     Summary: trying to detect cross-compilation
 int erreur; /* Error number */  
 int nvar;    Revision 1.172  2014/12/27 12:07:47  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.171  2014/12/23 13:26:59  brouard
 int ndeath=1; /* Number of dead states */    Summary: Back from Visual C
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Still problem with utsname.h on Windows
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.170  2014/12/23 11:17:12  brouard
 int maxwav; /* Maxim number of waves */    Summary: Cleaning some \%% back to %%
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.169  2014/12/22 23:08:31  brouard
 double jmean; /* Mean space between 2 waves */    Summary: 0.98p
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.168  2014/12/22 15:17:42  brouard
 FILE *ficreseij;    Summary: update
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.167  2014/12/22 13:50:56  brouard
   char fileresv[FILENAMELENGTH];    Summary: Testing uname and compiler version and if compiled 32 or 64
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Testing on Linux 64
   
 #define NR_END 1    Revision 1.166  2014/12/22 11:40:47  brouard
 #define FREE_ARG char*    *** empty log message ***
 #define FTOL 1.0e-10  
     Revision 1.165  2014/12/16 11:20:36  brouard
 #define NRANSI    Summary: After compiling on Visual C
 #define ITMAX 200  
     * imach.c (Module): Merging 1.61 to 1.162
 #define TOL 2.0e-4  
     Revision 1.164  2014/12/16 10:52:11  brouard
 #define CGOLD 0.3819660    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    * imach.c (Module): Merging 1.61 to 1.162
   
 #define GOLD 1.618034    Revision 1.163  2014/12/16 10:30:11  brouard
 #define GLIMIT 100.0    * imach.c (Module): Merging 1.61 to 1.162
 #define TINY 1.0e-20  
     Revision 1.162  2014/09/25 11:43:39  brouard
 static double maxarg1,maxarg2;    Summary: temporary backup 0.99!
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.1  2014/09/16 11:06:58  brouard
      Summary: With some code (wrong) for nlopt
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Author:
   
 static double sqrarg;    Revision 1.161  2014/09/15 20:41:41  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Summary: Problem with macro SQR on Intel compiler
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.160  2014/09/02 09:24:05  brouard
 int imx;    *** empty log message ***
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.159  2014/09/01 10:34:10  brouard
     Summary: WIN32
 int estepm;    Author: Brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.158  2014/08/27 17:11:51  brouard
 int m,nb;    *** empty log message ***
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.157  2014/08/27 16:26:55  brouard
 double **pmmij, ***probs, ***mobaverage;    Summary: Preparing windows Visual studio version
 double dateintmean=0;    Author: Brouard
   
 double *weight;    In order to compile on Visual studio, time.h is now correct and time_t
 int **s; /* Status */    and tm struct should be used. difftime should be used but sometimes I
 double *agedc, **covar, idx;    just make the differences in raw time format (time(&now).
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.155  2014/08/25 18:32:34  brouard
 {    Summary: New compile, minor changes
    char *s;                             /* pointer */    Author: Brouard
    int  l1, l2;                         /* length counters */  
     Revision 1.154  2014/06/20 17:32:08  brouard
    l1 = strlen( path );                 /* length of path */    Summary: Outputs now all graphs of convergence to period prevalence
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.153  2014/06/20 16:45:46  brouard
    s = strrchr( path, '\\' );           /* find last / */    Summary: If 3 live state, convergence to period prevalence on same graph
 #else    Author: Brouard
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.152  2014/06/18 17:54:09  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.151  2014/06/18 16:43:30  brouard
     *** empty log message ***
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.150  2014/06/18 16:42:35  brouard
       extern char       *getcwd( );    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.149  2014/06/18 15:51:14  brouard
          return( GLOCK_ERROR_GETCWD );    Summary: Some fixes in parameter files errors
       }    Author: Nicolas Brouard
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.148  2014/06/17 17:38:48  brouard
       s++;                              /* after this, the filename */    Summary: Nothing new
       l2 = strlen( s );                 /* length of filename */    Author: Brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Just a new packaging for OS/X version 0.98nS
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.147  2014/06/16 10:33:11  brouard
    }    *** empty log message ***
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.146  2014/06/16 10:20:28  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Summary: Merge
 #else    Author: Brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Merge, before building revised version.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.145  2014/06/10 21:23:15  brouard
    strcpy(ext,s);                       /* save extension */    Summary: Debugging with valgrind
    l1= strlen( name);    Author: Nicolas Brouard
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Lot of changes in order to output the results with some covariates
    finame[l1-l2]= 0;    After the Edimburgh REVES conference 2014, it seems mandatory to
    return( 0 );                         /* we're done */    improve the code.
 }    No more memory valgrind error but a lot has to be done in order to
     continue the work of splitting the code into subroutines.
     Also, decodemodel has been improved. Tricode is still not
 /******************************************/    optimal. nbcode should be improved. Documentation has been added in
     the source code.
 void replace(char *s, char*t)  
 {    Revision 1.143  2014/01/26 09:45:38  brouard
   int i;    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   int lg=20;  
   i=0;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   lg=strlen(t);    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.142  2014/01/26 03:57:36  brouard
     if (t[i]== '\\') s[i]='/';    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   }  
 }    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
 int nbocc(char *s, char occ)    Revision 1.141  2014/01/26 02:42:01  brouard
 {    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   int i,j=0;  
   int lg=20;    Revision 1.140  2011/09/02 10:37:54  brouard
   i=0;    Summary: times.h is ok with mingw32 now.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.139  2010/06/14 07:50:17  brouard
   if  (s[i] == occ ) j++;    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   }    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   return j;  
 }    Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.137  2010/04/29 18:11:38  brouard
   int i,lg,j,p=0;    (Module): Checking covariates for more complex models
   i=0;    than V1+V2. A lot of change to be done. Unstable.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.136  2010/04/26 20:30:53  brouard
   }    (Module): merging some libgsl code. Fixing computation
     of likelione (using inter/intrapolation if mle = 0) in order to
   lg=strlen(t);    get same likelihood as if mle=1.
   for(j=0; j<p; j++) {    Some cleaning of code and comments added.
     (u[j] = t[j]);  
   }    Revision 1.135  2009/10/29 15:33:14  brouard
      u[p]='\0';    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
    for(j=0; j<= lg; j++) {    Revision 1.134  2009/10/29 13:18:53  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    (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
 /********************** nrerror ********************/  
     Revision 1.132  2009/07/06 08:22:05  brouard
 void nrerror(char error_text[])    Many tings
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.131  2009/06/20 16:22:47  brouard
   fprintf(stderr,"%s\n",error_text);    Some dimensions resccaled
   exit(1);  
 }    Revision 1.130  2009/05/26 06:44:34  brouard
 /*********************** vector *******************/    (Module): Max Covariate is now set to 20 instead of 8. A
 double *vector(int nl, int nh)    lot of cleaning with variables initialized to 0. Trying to make
 {    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.129  2007/08/31 13:49:27  lievre
   if (!v) nrerror("allocation failure in vector");    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   return v-nl+NR_END;  
 }    Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.127  2006/04/28 18:11:50  brouard
 {    (Module): Yes the sum of survivors was wrong since
   free((FREE_ARG)(v+nl-NR_END));    imach-114 because nhstepm was no more computed in the age
 }    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
 /************************ivector *******************************/    compute health expectancies (without variances) in a first step
 int *ivector(long nl,long nh)    and then all the health expectancies with variances or standard
 {    deviation (needs data from the Hessian matrices) which slows the
   int *v;    computation.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    In the future we should be able to stop the program is only health
   if (!v) nrerror("allocation failure in ivector");    expectancies and graph are needed without standard deviations.
   return v-nl+NR_END;  
 }    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
 /******************free ivector **************************/    imach-114 because nhstepm was no more computed in the age
 void free_ivector(int *v, long nl, long nh)    loop. Now we define nhstepma in the age loop.
 {    Version 0.98h
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 /******************* imatrix *******************************/    Forecasting file added.
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.124  2006/03/22 17:13:53  lievre
 {    Parameters are printed with %lf instead of %f (more numbers after the comma).
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    The log-likelihood is printed in the log file
   int **m;  
      Revision 1.123  2006/03/20 10:52:43  brouard
   /* allocate pointers to rows */    * imach.c (Module): <title> changed, corresponds to .htm file
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    name. <head> headers where missing.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    * imach.c (Module): Weights can have a decimal point as for
   m -= nrl;    English (a comma might work with a correct LC_NUMERIC environment,
      otherwise the weight is truncated).
      Modification of warning when the covariates values are not 0 or
   /* allocate rows and set pointers to them */    1.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Version 0.98g
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.122  2006/03/20 09:45:41  brouard
   m[nrl] -= ncl;    (Module): Weights can have a decimal point as for
      English (a comma might work with a correct LC_NUMERIC environment,
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    otherwise the weight is truncated).
      Modification of warning when the covariates values are not 0 or
   /* return pointer to array of pointers to rows */    1.
   return m;    Version 0.98g
 }  
     Revision 1.121  2006/03/16 17:45:01  lievre
 /****************** free_imatrix *************************/    * imach.c (Module): Comments concerning covariates added
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    * imach.c (Module): refinements in the computation of lli if
       long nch,ncl,nrh,nrl;    status=-2 in order to have more reliable computation if stepm is
      /* free an int matrix allocated by imatrix() */    not 1 month. Version 0.98f
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Revision 1.120  2006/03/16 15:10:38  lievre
   free((FREE_ARG) (m+nrl-NR_END));    (Module): refinements in the computation of lli if
 }    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.119  2006/03/15 17:42:26  brouard
 {    (Module): Bug if status = -2, the loglikelihood was
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    computed as likelihood omitting the logarithm. Version O.98e
   double **m;  
     Revision 1.118  2006/03/14 18:20:07  brouard
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Module): varevsij Comments added explaining the second
   if (!m) nrerror("allocation failure 1 in matrix()");    table of variances if popbased=1 .
   m += NR_END;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   m -= nrl;    (Module): Function pstamp added
     (Module): Version 0.98d
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.117  2006/03/14 17:16:22  brouard
   m[nrl] += NR_END;    (Module): varevsij Comments added explaining the second
   m[nrl] -= ncl;    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    (Module): Function pstamp added
   return m;    (Module): Version 0.98d
 }  
     Revision 1.116  2006/03/06 10:29:27  brouard
 /*************************free matrix ************************/    (Module): Variance-covariance wrong links and
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    varian-covariance of ej. is needed (Saito).
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.115  2006/02/27 12:17:45  brouard
   free((FREE_ARG)(m+nrl-NR_END));    (Module): One freematrix added in mlikeli! 0.98c
 }  
     Revision 1.114  2006/02/26 12:57:58  brouard
 /******************* ma3x *******************************/    (Module): Some improvements in processing parameter
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    filename with strsep.
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.113  2006/02/24 14:20:24  brouard
   double ***m;    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    allocation too.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.112  2006/01/30 09:55:26  brouard
   m -= nrl;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.111  2006/01/25 20:38:18  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Lots of cleaning and bugs added (Gompertz)
   m[nrl] += NR_END;    (Module): Comments can be added in data file. Missing date values
   m[nrl] -= ncl;    can be a simple dot '.'.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Revision 1.109  2006/01/24 19:37:15  brouard
   m[nrl][ncl] += NR_END;    (Module): Comments (lines starting with a #) are allowed in data.
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.108  2006/01/19 18:05:42  lievre
     m[nrl][j]=m[nrl][j-1]+nlay;    Gnuplot problem appeared...
      To be fixed
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Revision 1.107  2006/01/19 16:20:37  brouard
     for (j=ncl+1; j<=nch; j++)    Test existence of gnuplot in imach path
       m[i][j]=m[i][j-1]+nlay;  
   }    Revision 1.106  2006/01/19 13:24:36  brouard
   return m;    Some cleaning and links added in html output
 }  
     Revision 1.105  2006/01/05 20:23:19  lievre
 /*************************free ma3x ************************/    *** empty log message ***
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    Revision 1.104  2005/09/30 16:11:43  lievre
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    (Module): sump fixed, loop imx fixed, and simplifications.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    (Module): If the status is missing at the last wave but we know
   free((FREE_ARG)(m+nrl-NR_END));    that the person is alive, then we can code his/her status as -2
 }    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 /***************** f1dim *************************/    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 extern int ncom;    the healthy state at last known wave). Version is 0.98
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    Revision 1.103  2005/09/30 15:54:49  lievre
      (Module): sump fixed, loop imx fixed, and simplifications.
 double f1dim(double x)  
 {    Revision 1.102  2004/09/15 17:31:30  brouard
   int j;    Add the possibility to read data file including tab characters.
   double f;  
   double *xt;    Revision 1.101  2004/09/15 10:38:38  brouard
      Fix on curr_time
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Revision 1.100  2004/07/12 18:29:06  brouard
   f=(*nrfunc)(xt);    Add version for Mac OS X. Just define UNIX in Makefile
   free_vector(xt,1,ncom);  
   return f;    Revision 1.99  2004/06/05 08:57:40  brouard
 }    *** empty log message ***
   
 /*****************brent *************************/    Revision 1.98  2004/05/16 15:05:56  brouard
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    New version 0.97 . First attempt to estimate force of mortality
 {    directly from the data i.e. without the need of knowing the health
   int iter;    state at each age, but using a Gompertz model: log u =a + b*age .
   double a,b,d,etemp;    This is the basic analysis of mortality and should be done before any
   double fu,fv,fw,fx;    other analysis, in order to test if the mortality estimated from the
   double ftemp;    cross-longitudinal survey is different from the mortality estimated
   double p,q,r,tol1,tol2,u,v,w,x,xm;    from other sources like vital statistic data.
   double e=0.0;  
      The same imach parameter file can be used but the option for mle should be -3.
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    Agnès, who wrote this part of the code, tried to keep most of the
   x=w=v=bx;    former routines in order to include the new code within the former code.
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    The output is very simple: only an estimate of the intercept and of
     xm=0.5*(a+b);    the slope with 95% confident intervals.
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    Current limitations:
     printf(".");fflush(stdout);    A) Even if you enter covariates, i.e. with the
 #ifdef DEBUG    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     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);    B) There is no computation of Life Expectancy nor Life Table.
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    Revision 1.97  2004/02/20 13:25:42  lievre
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    Version 0.96d. Population forecasting command line is (temporarily)
       *xmin=x;    suppressed.
       return fx;  
     }    Revision 1.96  2003/07/15 15:38:55  brouard
     ftemp=fu;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     if (fabs(e) > tol1) {    rewritten within the same printf. Workaround: many printfs.
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    Revision 1.95  2003/07/08 07:54:34  brouard
       p=(x-v)*q-(x-w)*r;    * imach.c (Repository):
       q=2.0*(q-r);    (Repository): Using imachwizard code to output a more meaningful covariance
       if (q > 0.0) p = -p;    matrix (cov(a12,c31) instead of numbers.
       q=fabs(q);  
       etemp=e;    Revision 1.94  2003/06/27 13:00:02  brouard
       e=d;    Just cleaning
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    Revision 1.93  2003/06/25 16:33:55  brouard
       else {    (Module): On windows (cygwin) function asctime_r doesn't
         d=p/q;    exist so I changed back to asctime which exists.
         u=x+d;    (Module): Version 0.96b
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    Revision 1.92  2003/06/25 16:30:45  brouard
       }    (Module): On windows (cygwin) function asctime_r doesn't
     } else {    exist so I changed back to asctime which exists.
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }    Revision 1.91  2003/06/25 15:30:29  brouard
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    * imach.c (Repository): Duplicated warning errors corrected.
     fu=(*f)(u);    (Repository): Elapsed time after each iteration is now output. It
     if (fu <= fx) {    helps to forecast when convergence will be reached. Elapsed time
       if (u >= x) a=x; else b=x;    is stamped in powell.  We created a new html file for the graphs
       SHFT(v,w,x,u)    concerning matrix of covariance. It has extension -cov.htm.
         SHFT(fv,fw,fx,fu)  
         } else {    Revision 1.90  2003/06/24 12:34:15  brouard
           if (u < x) a=u; else b=u;    (Module): Some bugs corrected for windows. Also, when
           if (fu <= fw || w == x) {    mle=-1 a template is output in file "or"mypar.txt with the design
             v=w;    of the covariance matrix to be input.
             w=u;  
             fv=fw;    Revision 1.89  2003/06/24 12:30:52  brouard
             fw=fu;    (Module): Some bugs corrected for windows. Also, when
           } else if (fu <= fv || v == x || v == w) {    mle=-1 a template is output in file "or"mypar.txt with the design
             v=u;    of the covariance matrix to be input.
             fv=fu;  
           }    Revision 1.88  2003/06/23 17:54:56  brouard
         }    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   }  
   nrerror("Too many iterations in brent");    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
     (Module): Change position of html and gnuplot routines and added
 /****************** mnbrak ***********************/    routine fileappend.
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Revision 1.85  2003/06/17 13:12:43  brouard
             double (*func)(double))    * imach.c (Repository): Check when date of death was earlier that
 {    current date of interview. It may happen when the death was just
   double ulim,u,r,q, dum;    prior to the death. In this case, dh was negative and likelihood
   double fu;    was wrong (infinity). We still send an "Error" but patch by
      assuming that the date of death was just one stepm after the
   *fa=(*func)(*ax);    interview.
   *fb=(*func)(*bx);    (Repository): Because some people have very long ID (first column)
   if (*fb > *fa) {    we changed int to long in num[] and we added a new lvector for
     SHFT(dum,*ax,*bx,dum)    memory allocation. But we also truncated to 8 characters (left
       SHFT(dum,*fb,*fa,dum)    truncation)
       }    (Repository): No more line truncation errors.
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);    Revision 1.84  2003/06/13 21:44:43  brouard
   while (*fb > *fc) {    * imach.c (Repository): Replace "freqsummary" at a correct
     r=(*bx-*ax)*(*fb-*fc);    place. It differs from routine "prevalence" which may be called
     q=(*bx-*cx)*(*fb-*fa);    many times. Probs is memory consuming and must be used with
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    parcimony.
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {    Revision 1.83  2003/06/10 13:39:11  lievre
       fu=(*func)(u);    *** empty log message ***
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);    Revision 1.82  2003/06/05 15:57:20  brouard
       if (fu < *fc) {    Add log in  imach.c and  fullversion number is now printed.
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  */
           }  /*
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {     Interpolated Markov Chain
       u=ulim;  
       fu=(*func)(u);    Short summary of the programme:
     } else {    
       u=(*cx)+GOLD*(*cx-*bx);    This program computes Healthy Life Expectancies from
       fu=(*func)(u);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     }    first survey ("cross") where individuals from different ages are
     SHFT(*ax,*bx,*cx,u)    interviewed on their health status or degree of disability (in the
       SHFT(*fa,*fb,*fc,fu)    case of a health survey which is our main interest) -2- at least a
       }    second wave of interviews ("longitudinal") which measure each change
 }    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 /*************** linmin ************************/    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 int ncom;    simplest model is the multinomial logistic model where pij is the
 double *pcom,*xicom;    probability to be observed in state j at the second wave
 double (*nrfunc)(double []);    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
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    'age' is age and 'sex' is a covariate. If you want to have a more
 {    complex model than "constant and age", you should modify the program
   double brent(double ax, double bx, double cx,    where the markup *Covariates have to be included here again* invites
                double (*f)(double), double tol, double *xmin);    you to do it.  More covariates you add, slower the
   double f1dim(double x);    convergence.
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));    The advantage of this computer programme, compared to a simple
   int j;    multinomial logistic model, is clear when the delay between waves is not
   double xx,xmin,bx,ax;    identical for each individual. Also, if a individual missed an
   double fx,fb,fa;    intermediate interview, the information is lost, but taken into
      account using an interpolation or extrapolation.  
   ncom=n;  
   pcom=vector(1,n);    hPijx is the probability to be observed in state i at age x+h
   xicom=vector(1,n);    conditional to the observed state i at age x. The delay 'h' can be
   nrfunc=func;    split into an exact number (nh*stepm) of unobserved intermediate
   for (j=1;j<=n;j++) {    states. This elementary transition (by month, quarter,
     pcom[j]=p[j];    semester or year) is modelled as a multinomial logistic.  The hPx
     xicom[j]=xi[j];    matrix is simply the matrix product of nh*stepm elementary matrices
   }    and the contribution of each individual to the likelihood is simply
   ax=0.0;    hPijx.
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    Also this programme outputs the covariance matrix of the parameters but also
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    of the life expectancies. It also computes the period (stable) prevalence. 
 #ifdef DEBUG    
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #endif             Institut national d'études démographiques, Paris.
   for (j=1;j<=n;j++) {    This software have been partly granted by Euro-REVES, a concerted action
     xi[j] *= xmin;    from the European Union.
     p[j] += xi[j];    It is copyrighted identically to a GNU software product, ie programme and
   }    software can be distributed freely for non commercial use. Latest version
   free_vector(xicom,1,n);    can be accessed at http://euroreves.ined.fr/imach .
   free_vector(pcom,1,n);  
 }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 /*************** powell ************************/    
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    **********************************************************************/
             double (*func)(double []))  /*
 {    main
   void linmin(double p[], double xi[], int n, double *fret,    read parameterfile
               double (*func)(double []));    read datafile
   int i,ibig,j;    concatwav
   double del,t,*pt,*ptt,*xit;    freqsummary
   double fp,fptt;    if (mle >= 1)
   double *xits;      mlikeli
   pt=vector(1,n);    print results files
   ptt=vector(1,n);    if mle==1 
   xit=vector(1,n);       computes hessian
   xits=vector(1,n);    read end of parameter file: agemin, agemax, bage, fage, estepm
   *fret=(*func)(p);        begin-prev-date,...
   for (j=1;j<=n;j++) pt[j]=p[j];    open gnuplot file
   for (*iter=1;;++(*iter)) {    open html file
     fp=(*fret);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
     ibig=0;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
     del=0.0;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      freexexit2 possible for memory heap.
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);    h Pij x                         | pij_nom  ficrestpij
     printf("\n");     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
     for (i=1;i<=n;i++) {         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
       for (j=1;j<=n;j++) xit[j]=xi[j][i];         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       fptt=(*fret);  
 #ifdef DEBUG         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       printf("fret=%lf \n",*fret);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
 #endif    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
       printf("%d",i);fflush(stdout);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       linmin(p,xit,n,fret,func);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));    forecasting if prevfcast==1 prevforecast call prevalence()
         ibig=i;    health expectancies
       }    Variance-covariance of DFLE
 #ifdef DEBUG    prevalence()
       printf("%d %.12e",i,(*fret));     movingaverage()
       for (j=1;j<=n;j++) {    varevsij() 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    if popbased==1 varevsij(,popbased)
         printf(" x(%d)=%.12e",j,xit[j]);    total life expectancies
       }    Variance of period (stable) prevalence
       for(j=1;j<=n;j++)   end
         printf(" p=%.12e",p[j]);  */
       printf("\n");  
 #endif  /* #define DEBUG */
     }  /* #define DEBUGBRENT */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define POWELL /* Instead of NLOPT */
 #ifdef DEBUG  #define POWELLF1F3 /* Skip test */
       int k[2],l;  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
       k[0]=1;  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  #include <math.h>
       for (j=1;j<=n;j++)  #include <stdio.h>
         printf(" %.12e",p[j]);  #include <stdlib.h>
       printf("\n");  #include <string.h>
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  #ifdef _WIN32
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #include <io.h>
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #include <windows.h>
         }  #include <tchar.h>
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #else
       }  #include <unistd.h>
 #endif  #endif
   
   #include <limits.h>
       free_vector(xit,1,n);  #include <sys/types.h>
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  #if defined(__GNUC__)
       free_vector(pt,1,n);  #include <sys/utsname.h> /* Doesn't work on Windows */
       return;  #endif
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #include <sys/stat.h>
     for (j=1;j<=n;j++) {  #include <errno.h>
       ptt[j]=2.0*p[j]-pt[j];  /* extern int errno; */
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  /* #ifdef LINUX */
     }  /* #include <time.h> */
     fptt=(*func)(ptt);  /* #include "timeval.h" */
     if (fptt < fp) {  /* #else */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /* #include <sys/time.h> */
       if (t < 0.0) {  /* #endif */
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  #include <time.h>
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  #ifdef GSL
         }  #include <gsl/gsl_errno.h>
 #ifdef DEBUG  #include <gsl/gsl_multimin.h>
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #endif
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  
         printf("\n");  #ifdef NLOPT
 #endif  #include <nlopt.h>
       }  typedef struct {
     }    double (* function)(double [] );
   }  } myfunc_data ;
 }  #endif
   
 /**** Prevalence limit ****************/  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   int i, ii,j,k;  #define FILENAMELENGTH 132
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   double **out, cov[NCOVMAX], **pmij();  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  #define NINTERVMAX 8
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     }  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
    cov[1]=1.;  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
    #define MAXN 20000
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #define YEARM 12. /**< Number of months per year */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #define AGESUP 130
     newm=savm;  #define AGEBASE 40
     /* Covariates have to be included here again */  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
      cov[2]=agefin;  #ifdef _WIN32
    #define DIRSEPARATOR '\\'
       for (k=1; k<=cptcovn;k++) {  #define CHARSEPARATOR "\\"
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #define ODIRSEPARATOR '/'
         /*      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]]);*/  #else
       }  #define DIRSEPARATOR '/'
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #define CHARSEPARATOR "/"
       for (k=1; k<=cptcovprod;k++)  #define ODIRSEPARATOR '\\'
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #endif
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /* $Id$ */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /* $State$ */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  char version[]="Imach version 0.98q4, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
   char fullversion[]="$Revision$ $Date$"; 
     savm=oldm;  char strstart[80];
     oldm=newm;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
     maxmax=0.;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     for(j=1;j<=nlstate;j++){  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
       min=1.;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       max=0.;  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
       for(i=1; i<=nlstate; i++) {  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
         sumnew=0;  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
         prlim[i][j]= newm[i][j]/(1-sumnew);  int cptcovprodnoage=0; /**< Number of covariate products without age */   
         max=FMAX(max,prlim[i][j]);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
         min=FMIN(min,prlim[i][j]);  int cptcov=0; /* Working variable */
       }  int npar=NPARMAX;
       maxmin=max-min;  int nlstate=2; /* Number of live states */
       maxmax=FMAX(maxmax,maxmin);  int ndeath=1; /* Number of dead states */
     }  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     if(maxmax < ftolpl){  int popbased=0;
       return prlim;  
     }  int *wav; /* Number of waves for this individuual 0 is possible */
   }  int maxwav=0; /* Maxim number of waves */
 }  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 /*************** transition probabilities ***************/  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  int mle=1, weightopt=0;
 {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double s1, s2;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   /*double t34;*/  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   int i,j,j1, nc, ii, jj;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   int countcallfunc=0;  /* Count the number of calls to func */
     for(i=1; i<= nlstate; i++){  double jmean=1; /* Mean space between 2 waves */
     for(j=1; j<i;j++){  double **matprod2(); /* test */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  double **oldm, **newm, **savm; /* Working pointers to matrices */
         /*s2 += param[i][j][nc]*cov[nc];*/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*FILE *fic ; */ /* Used in readdata only */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       }  FILE *ficlog, *ficrespow;
       ps[i][j]=s2;  int globpr=0; /* Global variable for printing or not */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  double fretone; /* Only one call to likelihood */
     }  long ipmx=0; /* Number of contributions */
     for(j=i+1; j<=nlstate+ndeath;j++){  double sw; /* Sum of weights */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  char filerespow[FILENAMELENGTH];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  FILE *ficresilk;
       }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       ps[i][j]=s2;  FILE *ficresprobmorprev;
     }  FILE *fichtm, *fichtmcov; /* Html File */
   }  FILE *ficreseij;
     /*ps[3][2]=1;*/  char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
   for(i=1; i<= nlstate; i++){  char fileresstde[FILENAMELENGTH];
      s1=0;  FILE *ficrescveij;
     for(j=1; j<i; j++)  char filerescve[FILENAMELENGTH];
       s1+=exp(ps[i][j]);  FILE  *ficresvij;
     for(j=i+1; j<=nlstate+ndeath; j++)  char fileresv[FILENAMELENGTH];
       s1+=exp(ps[i][j]);  FILE  *ficresvpl;
     ps[i][i]=1./(s1+1.);  char fileresvpl[FILENAMELENGTH];
     for(j=1; j<i; j++)  char title[MAXLINE];
       ps[i][j]= exp(ps[i][j])*ps[i][i];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     for(j=i+1; j<=nlstate+ndeath; j++)  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       ps[i][j]= exp(ps[i][j])*ps[i][i];  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  char command[FILENAMELENGTH];
   } /* end i */  int  outcmd=0;
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  char filelog[FILENAMELENGTH]; /* Log file */
       ps[ii][ii]=1;  char filerest[FILENAMELENGTH];
     }  char fileregp[FILENAMELENGTH];
   }  char popfile[FILENAMELENGTH];
   
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
      printf("%lf ",ps[ii][jj]);  /* struct timezone tzp; */
    }  /* extern int gettimeofday(); */
     printf("\n ");  struct tm tml, *gmtime(), *localtime();
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  extern time_t time();
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   goto end;*/  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     return ps;  struct tm tm;
 }  
   char strcurr[80], strfor[80];
 /**************** Product of 2 matrices ******************/  
   char *endptr;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  long lval;
 {  double dval;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  #define NR_END 1
   /* in, b, out are matrice of pointers which should have been initialized  #define FREE_ARG char*
      before: only the contents of out is modified. The function returns  #define FTOL 1.0e-10
      a pointer to pointers identical to out */  
   long i, j, k;  #define NRANSI 
   for(i=nrl; i<= nrh; i++)  #define ITMAX 200 
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  #define TOL 2.0e-4 
         out[i][k] +=in[i][j]*b[j][k];  
   #define CGOLD 0.3819660 
   return out;  #define ZEPS 1.0e-10 
 }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
   #define GOLD 1.618034 
 /************* Higher Matrix Product ***************/  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  static double maxarg1,maxarg2;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
      duration (i.e. until  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
      (typically every 2 years instead of every month which is too big).  #define rint(a) floor(a+0.5)
      Model is determined by parameters x and covariates have to be  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
      included manually here.  #define mytinydouble 1.0e-16
   /* #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; */
   int i, j, d, h, k;  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   double **out, cov[NCOVMAX];  static double sqrarg;
   double **newm;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   /* Hstepm could be zero and should return the unit matrix */  int agegomp= AGEGOMP;
   for (i=1;i<=nlstate+ndeath;i++)  
     for (j=1;j<=nlstate+ndeath;j++){  int imx; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  int stepm=1;
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /* Stepm, step in month: minimum step interpolation*/
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int estepm;
   for(h=1; h <=nhstepm; h++){  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     for(d=1; d <=hstepm; d++){  
       newm=savm;  int m,nb;
       /* Covariates have to be included here again */  long *num;
       cov[1]=1.;  int firstpass=0, lastpass=4,*cod, *Tage,*cens;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];                     covariate for which somebody answered excluding 
       for (k=1; k<=cptcovage;k++)                     undefined. Usually 2: 0 and 1. */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
       for (k=1; k<=cptcovprod;k++)                               covariate for which somebody answered including 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];                               undefined. Usually 3: -1, 0 and 1. */
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  double *ageexmed,*agecens;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  double dateintmean=0;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  double *weight;
       savm=oldm;  int **s; /* Status */
       oldm=newm;  double *agedc;
     }  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
     for(i=1; i<=nlstate+ndeath; i++)                    * covar=matrix(0,NCOVMAX,1,n); 
       for(j=1;j<=nlstate+ndeath;j++) {                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
         po[i][j][h]=newm[i][j];  double  idx; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
          */  int *Ndum; /** Freq of modality (tricode */
       }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   } /* end h */  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   return po;  double *lsurv, *lpop, *tpop;
 }  
   double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double ftolhess; /**< Tolerance for computing hessian */
 /*************** log-likelihood *************/  
 double func( double *x)  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int i, ii, j, k, mi, d, kk;  {
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double **out;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double sw; /* Sum of weights */    */ 
   double lli; /* Individual log likelihood */    char  *ss;                            /* pointer */
   long ipmx;    int   l1=0, l2=0;                             /* length counters */
   /*extern weight */  
   /* We are differentiating ll according to initial status */    l1 = strlen(path );                   /* length of path */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   /*for(i=1;i<imx;i++)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     printf(" %d\n",s[4][i]);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   */      strcpy( name, path );               /* we got the fullname name because no directory */
   cov[1]=1.;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for(k=1; k<=nlstate; k++) ll[k]=0.;      /* get current working directory */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      /*    extern  char* getcwd ( char *buf , int len);*/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  #ifdef WIN32
     for(mi=1; mi<= wav[i]-1; mi++){      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
       for (ii=1;ii<=nlstate+ndeath;ii++)  #else
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          if (getcwd(dirc, FILENAME_MAX) == NULL) {
       for(d=0; d<dh[mi][i]; d++){  #endif
         newm=savm;        return( GLOCK_ERROR_GETCWD );
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      }
         for (kk=1; kk<=cptcovage;kk++) {      /* got dirc from getcwd*/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      printf(" DIRC = %s \n",dirc);
         }    } else {                              /* strip direcotry from path */
              ss++;                               /* after this, the filename */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      l2 = strlen( ss );                  /* length of filename */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         savm=oldm;      strcpy( name, ss );         /* save file name */
         oldm=newm;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
              dirc[l1-l2] = '\0';                 /* add zero */
              printf(" DIRC2 = %s \n",dirc);
       } /* end mult */    }
          /* We add a separator at the end of dirc if not exists */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    l1 = strlen( dirc );                  /* length of directory */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    if( dirc[l1-1] != DIRSEPARATOR ){
       ipmx +=1;      dirc[l1] =  DIRSEPARATOR;
       sw += weight[i];      dirc[l1+1] = 0; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      printf(" DIRC3 = %s \n",dirc);
     } /* end of wave */    }
   } /* end of individual */    ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      ss++;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      strcpy(ext,ss);                     /* save extension */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      l1= strlen( name);
   return -l;      l2= strlen(ss)+1;
 }      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
     }
 /*********** Maximum Likelihood Estimation ***************/  
     return( 0 );                          /* we're done */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  }
 {  
   int i,j, iter;  
   double **xi,*delti;  /******************************************/
   double fret;  
   xi=matrix(1,npar,1,npar);  void replace_back_to_slash(char *s, char*t)
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++)    int i;
       xi[i][j]=(i==j ? 1.0 : 0.0);    int lg=0;
   printf("Powell\n");    i=0;
   powell(p,xi,npar,ftol,&iter,&fret,func);    lg=strlen(t);
     for(i=0; i<= lg; i++) {
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      (s[i] = t[i]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      if (t[i]== '\\') s[i]='/';
     }
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  char *trimbb(char *out, char *in)
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
 {    char *s;
   double  **a,**y,*x,pd;    s=out;
   double **hess;    while (*in != '\0'){
   int i, j,jk;      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   int *indx;        in++;
       }
   double hessii(double p[], double delta, int theta, double delti[]);      *out++ = *in++;
   double hessij(double p[], double delti[], int i, int j);    }
   void lubksb(double **a, int npar, int *indx, double b[]) ;    *out='\0';
   void ludcmp(double **a, int npar, int *indx, double *d) ;    return s;
   }
   hess=matrix(1,npar,1,npar);  
   /* char *substrchaine(char *out, char *in, char *chain) */
   printf("\nCalculation of the hessian matrix. Wait...\n");  /* { */
   for (i=1;i<=npar;i++){  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
     printf("%d",i);fflush(stdout);  /*   char *s, *t; */
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*   t=in;s=out; */
     /*printf(" %f ",p[i]);*/  /*   while ((*in != *chain) && (*in != '\0')){ */
     /*printf(" %lf ",hess[i][i]);*/  /*     *out++ = *in++; */
   }  /*   } */
    
   for (i=1;i<=npar;i++) {  /*   /\* *in matches *chain *\/ */
     for (j=1;j<=npar;j++)  {  /*   while ((*in++ == *chain++) && (*in != '\0')){ */
       if (j>i) {  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
         printf(".%d%d",i,j);fflush(stdout);  /*   } */
         hess[i][j]=hessij(p,delti,i,j);  /*   in--; chain--; */
         hess[j][i]=hess[i][j];      /*   while ( (*in != '\0')){ */
         /*printf(" %lf ",hess[i][j]);*/  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
       }  /*     *out++ = *in++; */
     }  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   }  /*   } */
   printf("\n");  /*   *out='\0'; */
   /*   out=s; */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /*   return out; */
    /* } */
   a=matrix(1,npar,1,npar);  char *substrchaine(char *out, char *in, char *chain)
   y=matrix(1,npar,1,npar);  {
   x=vector(1,npar);    /* Substract chain 'chain' from 'in', return and output 'out' */
   indx=ivector(1,npar);    /* in="V1+V1*age+age*age+V2", chain="age*age" */
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    char *strloc;
   ludcmp(a,npar,indx,&pd);  
     strcpy (out, in); 
   for (j=1;j<=npar;j++) {    strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
     for (i=1;i<=npar;i++) x[i]=0;    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
     x[j]=1;    if(strloc != NULL){ 
     lubksb(a,npar,indx,x);      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
     for (i=1;i<=npar;i++){      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
       matcov[i][j]=x[i];      /* strcpy (strloc, strloc +strlen(chain));*/
     }    }
   }    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
     return out;
   printf("\n#Hessian matrix#\n");  }
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  char *cutl(char *blocc, char *alocc, char *in, char occ)
     }  {
     printf("\n");    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
   }       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef" and alocc="ghi2j".
   /* Recompute Inverse */       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   for (i=1;i<=npar;i++)    */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    char *s, *t;
   ludcmp(a,npar,indx,&pd);    t=in;s=in;
     while ((*in != occ) && (*in != '\0')){
   /*  printf("\n#Hessian matrix recomputed#\n");      *alocc++ = *in++;
     }
   for (j=1;j<=npar;j++) {    if( *in == occ){
     for (i=1;i<=npar;i++) x[i]=0;      *(alocc)='\0';
     x[j]=1;      s=++in;
     lubksb(a,npar,indx,x);    }
     for (i=1;i<=npar;i++){   
       y[i][j]=x[i];    if (s == t) {/* occ not found */
       printf("%.3e ",y[i][j]);      *(alocc-(in-s))='\0';
     }      in=s;
     printf("\n");    }
   }    while ( *in != '\0'){
   */      *blocc++ = *in++;
     }
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);    *blocc='\0';
   free_vector(x,1,npar);    return t;
   free_ivector(indx,1,npar);  }
   free_matrix(hess,1,npar,1,npar);  char *cutv(char *blocc, char *alocc, char *in, char occ)
   {
     /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
 }       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
 /*************** hessian matrix ****************/       If occ is not found blocc is null and alocc is equal to in. Returns alocc
 double hessii( double x[], double delta, int theta, double delti[])    */
 {    char *s, *t;
   int i;    t=in;s=in;
   int l=1, lmax=20;    while (*in != '\0'){
   double k1,k2;      while( *in == occ){
   double p2[NPARMAX+1];        *blocc++ = *in++;
   double res;        s=in;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      }
   double fx;      *blocc++ = *in++;
   int k=0,kmax=10;    }
   double l1;    if (s == t) /* occ not found */
       *(blocc-(in-s))='\0';
   fx=func(x);    else
   for (i=1;i<=npar;i++) p2[i]=x[i];      *(blocc-(in-s)-1)='\0';
   for(l=0 ; l <=lmax; l++){    in=s;
     l1=pow(10,l);    while ( *in != '\0'){
     delts=delt;      *alocc++ = *in++;
     for(k=1 ; k <kmax; k=k+1){    }
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;    *alocc='\0';
       k1=func(p2)-fx;    return s;
       p2[theta]=x[theta]-delt;  }
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */  int nbocc(char *s, char occ)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  {
          int i,j=0;
 #ifdef DEBUG    int lg=20;
       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);    i=0;
 #endif    lg=strlen(s);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    for(i=0; i<= lg; i++) {
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    if  (s[i] == occ ) j++;
         k=kmax;    }
       }    return j;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  }
         k=kmax; l=lmax*10.;  
       }  /* void cutv(char *u,char *v, char*t, char occ) */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  /* { */
         delts=delt;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     }  /*      gives u="abcdef2ghi" and v="j" *\/ */
   }  /*   int i,lg,j,p=0; */
   delti[theta]=delts;  /*   i=0; */
   return res;  /*   lg=strlen(t); */
    /*   for(j=0; j<=lg-1; j++) { */
 }  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*   } */
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {  /*   for(j=0; j<p; j++) { */
   int i;  /*     (u[j] = t[j]); */
   int l=1, l1, lmax=20;  /*   } */
   double k1,k2,k3,k4,res,fx;  /*      u[p]='\0'; */
   double p2[NPARMAX+1];  
   int k;  /*    for(j=0; j<= lg; j++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   fx=func(x);  /*   } */
   for (k=1; k<=2; k++) {  /* } */
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  #ifdef _WIN32
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  char * strsep(char **pp, const char *delim)
     k1=func(p2)-fx;  {
      char *p, *q;
     p2[thetai]=x[thetai]+delti[thetai]/k;           
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    if ((p = *pp) == NULL)
     k2=func(p2)-fx;      return 0;
      if ((q = strpbrk (p, delim)) != NULL)
     p2[thetai]=x[thetai]-delti[thetai]/k;    {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      *pp = q + 1;
     k3=func(p2)-fx;      *q = '\0';
      }
     p2[thetai]=x[thetai]-delti[thetai]/k;    else
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      *pp = 0;
     k4=func(p2)-fx;    return p;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  }
 #ifdef DEBUG  #endif
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif  /********************** nrerror ********************/
   }  
   return res;  void nrerror(char error_text[])
 }  {
     fprintf(stderr,"ERREUR ...\n");
 /************** Inverse of matrix **************/    fprintf(stderr,"%s\n",error_text);
 void ludcmp(double **a, int n, int *indx, double *d)    exit(EXIT_FAILURE);
 {  }
   int i,imax,j,k;  /*********************** vector *******************/
   double big,dum,sum,temp;  double *vector(int nl, int nh)
   double *vv;  {
      double *v;
   vv=vector(1,n);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   *d=1.0;    if (!v) nrerror("allocation failure in vector");
   for (i=1;i<=n;i++) {    return v-nl+NR_END;
     big=0.0;  }
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;  /************************ free vector ******************/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  void free_vector(double*v, int nl, int nh)
     vv[i]=1.0/big;  {
   }    free((FREE_ARG)(v+nl-NR_END));
   for (j=1;j<=n;j++) {  }
     for (i=1;i<j;i++) {  
       sum=a[i][j];  /************************ivector *******************************/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  int *ivector(long nl,long nh)
       a[i][j]=sum;  {
     }    int *v;
     big=0.0;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     for (i=j;i<=n;i++) {    if (!v) nrerror("allocation failure in ivector");
       sum=a[i][j];    return v-nl+NR_END;
       for (k=1;k<j;k++)  }
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /******************free ivector **************************/
       if ( (dum=vv[i]*fabs(sum)) >= big) {  void free_ivector(int *v, long nl, long nh)
         big=dum;  {
         imax=i;    free((FREE_ARG)(v+nl-NR_END));
       }  }
     }  
     if (j != imax) {  /************************lvector *******************************/
       for (k=1;k<=n;k++) {  long *lvector(long nl,long nh)
         dum=a[imax][k];  {
         a[imax][k]=a[j][k];    long *v;
         a[j][k]=dum;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       }    if (!v) nrerror("allocation failure in ivector");
       *d = -(*d);    return v-nl+NR_END;
       vv[imax]=vv[j];  }
     }  
     indx[j]=imax;  /******************free lvector **************************/
     if (a[j][j] == 0.0) a[j][j]=TINY;  void free_lvector(long *v, long nl, long nh)
     if (j != n) {  {
       dum=1.0/(a[j][j]);    free((FREE_ARG)(v+nl-NR_END));
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  }
     }  
   }  /******************* imatrix *******************************/
   free_vector(vv,1,n);  /* Doesn't work */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 ;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 }  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 void lubksb(double **a, int n, int *indx, double b[])    int **m; 
 {    
   int i,ii=0,ip,j;    /* allocate pointers to rows */ 
   double sum;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
      if (!m) nrerror("allocation failure 1 in matrix()"); 
   for (i=1;i<=n;i++) {    m += NR_END; 
     ip=indx[i];    m -= nrl; 
     sum=b[ip];    
     b[ip]=b[i];    
     if (ii)    /* allocate rows and set pointers to them */ 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     else if (sum) ii=i;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     b[i]=sum;    m[nrl] += NR_END; 
   }    m[nrl] -= ncl; 
   for (i=n;i>=1;i--) {    
     sum=b[i];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    
     b[i]=sum/a[i][i];    /* return pointer to array of pointers to rows */ 
   }    return m; 
 }  } 
   
 /************ Frequencies ********************/  /****************** free_imatrix *************************/
 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)  void free_imatrix(m,nrl,nrh,ncl,nch)
 {  /* Some frequencies */        int **m;
          long nch,ncl,nrh,nrl; 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;       /* free an int matrix allocated by imatrix() */ 
   double ***freq; /* Frequencies */  { 
   double *pp;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double pos, k2, dateintsum=0,k2cpt=0;    free((FREE_ARG) (m+nrl-NR_END)); 
   FILE *ficresp;  } 
   char fileresp[FILENAMELENGTH];  
    /******************* matrix *******************************/
   pp=vector(1,nlstate);  double **matrix(long nrl, long nrh, long ncl, long nch)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
   strcpy(fileresp,"p");    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   strcat(fileresp,fileres);    double **m;
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     exit(0);    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    m -= nrl;
   j1=0;  
      m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   j=cptcoveff;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    m[nrl] += NR_END;
      m[nrl] -= ncl;
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       j1++;    return m;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
         scanf("%d", i);*/  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
       for (i=-1; i<=nlstate+ndeath; i++)    that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
         for (jk=-1; jk<=nlstate+ndeath; jk++)       */
           for(m=agemin; m <= agemax+3; m++)  }
             freq[i][jk][m]=0;  
        /*************************free matrix ************************/
       dateintsum=0;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       k2cpt=0;  {
       for (i=1; i<=imx; i++) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         bool=1;    free((FREE_ARG)(m+nrl-NR_END));
         if  (cptcovn>0) {  }
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  /******************* ma3x *******************************/
               bool=0;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         }  {
         if (bool==1) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
           for(m=firstpass; m<=lastpass; m++){    double ***m;
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
               if(agev[m][i]==0) agev[m][i]=agemax+1;    if (!m) nrerror("allocation failure 1 in matrix()");
               if(agev[m][i]==1) agev[m][i]=agemax+2;    m += NR_END;
               if (m<lastpass) {    m -= nrl;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
               }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                  m[nrl] += NR_END;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    m[nrl] -= ncl;
                 dateintsum=dateintsum+k2;  
                 k2cpt++;    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 (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         }    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
            for (j=ncl+1; j<=nch; j++) 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      m[nrl][j]=m[nrl][j-1]+nlay;
     
       if  (cptcovn>0) {    for (i=nrl+1; i<=nrh; i++) {
         fprintf(ficresp, "\n#********** Variable ");      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      for (j=ncl+1; j<=nch; j++) 
         fprintf(ficresp, "**********\n#");        m[i][j]=m[i][j-1]+nlay;
       }    }
       for(i=1; i<=nlstate;i++)    return m; 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       fprintf(ficresp, "\n");             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
          */
       for(i=(int)agemin; i <= (int)agemax+3; i++){  }
         if(i==(int)agemax+3)  
           printf("Total");  /*************************free ma3x ************************/
         else  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
           printf("Age %d", i);  {
         for(jk=1; jk <=nlstate ; jk++){    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
             pp[jk] += freq[jk][m][i];    free((FREE_ARG)(m+nrl-NR_END));
         }  }
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  /*************** function subdirf ***********/
             pos += freq[jk][m][i];  char *subdirf(char fileres[])
           if(pp[jk]>=1.e-10)  {
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    /* Caution optionfilefiname is hidden */
           else    strcpy(tmpout,optionfilefiname);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    strcat(tmpout,"/"); /* Add to the right */
         }    strcat(tmpout,fileres);
     return tmpout;
         for(jk=1; jk <=nlstate ; jk++){  }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];  /*************** function subdirf2 ***********/
         }  char *subdirf2(char fileres[], char *preop)
   {
         for(jk=1,pos=0; jk <=nlstate ; jk++)    
           pos += pp[jk];    /* Caution optionfilefiname is hidden */
         for(jk=1; jk <=nlstate ; jk++){    strcpy(tmpout,optionfilefiname);
           if(pos>=1.e-5)    strcat(tmpout,"/");
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    strcat(tmpout,preop);
           else    strcat(tmpout,fileres);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    return tmpout;
           if( i <= (int) agemax){  }
             if(pos>=1.e-5){  
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  /*************** function subdirf3 ***********/
               probs[i][jk][j1]= pp[jk]/pos;  char *subdirf3(char fileres[], char *preop, char *preop2)
               /*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    /* Caution optionfilefiname is hidden */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    strcpy(tmpout,optionfilefiname);
           }    strcat(tmpout,"/");
         }    strcat(tmpout,preop);
            strcat(tmpout,preop2);
         for(jk=-1; jk <=nlstate+ndeath; jk++)    strcat(tmpout,fileres);
           for(m=-1; m <=nlstate+ndeath; m++)    return tmpout;
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  }
         if(i <= (int) agemax)  
           fprintf(ficresp,"\n");  char *asc_diff_time(long time_sec, char ascdiff[])
         printf("\n");  {
       }    long sec_left, days, hours, minutes;
     }    days = (time_sec) / (60*60*24);
   }    sec_left = (time_sec) % (60*60*24);
   dateintmean=dateintsum/k2cpt;    hours = (sec_left) / (60*60) ;
      sec_left = (sec_left) %(60*60);
   fclose(ficresp);    minutes = (sec_left) /60;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    sec_left = (sec_left) % (60);
   free_vector(pp,1,nlstate);    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
      return ascdiff;
   /* End of Freq */  }
 }  
   /***************** f1dim *************************/
 /************ Prevalence ********************/  extern int ncom; 
 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)  extern double *pcom,*xicom;
 {  /* Some frequencies */  extern double (*nrfunc)(double []); 
     
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  double f1dim(double x) 
   double ***freq; /* Frequencies */  { 
   double *pp;    int j; 
   double pos, k2;    double f;
     double *xt; 
   pp=vector(1,nlstate);   
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    xt=vector(1,ncom); 
      for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    f=(*nrfunc)(xt); 
   j1=0;    free_vector(xt,1,ncom); 
      return f; 
   j=cptcoveff;  } 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
    /*****************brent *************************/
   for(k1=1; k1<=j;k1++){  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for(i1=1; i1<=ncodemax[k1];i1++){  {
       j1++;    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
           * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
       for (i=-1; i<=nlstate+ndeath; i++)       * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
         for (jk=-1; jk<=nlstate+ndeath; jk++)       * the minimum is returned as xmin, and the minimum function value is returned as brent , the
           for(m=agemin; m <= agemax+3; m++)     * returned function value. 
             freq[i][jk][m]=0;    */
          int iter; 
       for (i=1; i<=imx; i++) {    double a,b,d,etemp;
         bool=1;    double fu=0,fv,fw,fx;
         if  (cptcovn>0) {    double ftemp=0.;
           for (z1=1; z1<=cptcoveff; z1++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double e=0.0; 
               bool=0;   
         }    a=(ax < cx ? ax : cx); 
         if (bool==1) {    b=(ax > cx ? ax : cx); 
           for(m=firstpass; m<=lastpass; m++){    x=w=v=bx; 
             k2=anint[m][i]+(mint[m][i]/12.);    fw=fv=fx=(*f)(x); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    for (iter=1;iter<=ITMAX;iter++) { 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      xm=0.5*(a+b); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
               if (m<lastpass) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                 if (calagedate>0)      printf(".");fflush(stdout);
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      fprintf(ficlog,".");fflush(ficlog);
                 else  #ifdef DEBUGBRENT
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[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);
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[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);
               }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
             }  #endif
           }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         }        *xmin=x; 
       }        return fx; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){      } 
         for(jk=1; jk <=nlstate ; jk++){      ftemp=fu;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      if (fabs(e) > tol1) { 
             pp[jk] += freq[jk][m][i];        r=(x-w)*(fx-fv); 
         }        q=(x-v)*(fx-fw); 
         for(jk=1; jk <=nlstate ; jk++){        p=(x-v)*q-(x-w)*r; 
           for(m=-1, pos=0; m <=0 ; m++)        q=2.0*(q-r); 
             pos += freq[jk][m][i];        if (q > 0.0) p = -p; 
         }        q=fabs(q); 
                etemp=e; 
         for(jk=1; jk <=nlstate ; jk++){        e=d; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
             pp[jk] += freq[jk][m][i];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         }        else { 
                  d=p/q; 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          u=x+d; 
                  if (u-a < tol2 || b-u < tol2) 
         for(jk=1; jk <=nlstate ; jk++){                d=SIGN(tol1,xm-x); 
           if( i <= (int) agemax){        } 
             if(pos>=1.e-5){      } else { 
               probs[i][jk][j1]= pp[jk]/pos;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             }      } 
           }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         }      fu=(*f)(u); 
              if (fu <= fx) { 
       }        if (u >= x) a=x; else b=x; 
     }        SHFT(v,w,x,u) 
   }        SHFT(fv,fw,fx,fu) 
       } else { 
          if (u < x) a=u; else b=u; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        if (fu <= fw || w == x) { 
   free_vector(pp,1,nlstate);          v=w; 
            w=u; 
 }  /* End of Freq */          fv=fw; 
           fw=fu; 
 /************* Waves Concatenation ***************/        } else if (fu <= fv || v == x || v == w) { 
           v=u; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          fv=fu; 
 {        } 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      } 
      Death is a valid wave (if date is known).    } 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    nrerror("Too many iterations in brent"); 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    *xmin=x; 
      and mw[mi+1][i]. dh depends on stepm.    return fx; 
      */  } 
   
   int i, mi, m;  /****************** mnbrak ***********************/
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   int j, k=0,jk, ju, jl;  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
   double sum=0.;  the downhill direction (defined by the function as evaluated at the initial points) and returns
   jmin=1e+5;  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
   jmax=-1;  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
   jmean=0.;     */
   for(i=1; i<=imx; i++){    double ulim,u,r,q, dum;
     mi=0;    double fu; 
     m=firstpass;  
     while(s[m][i] <= nlstate){    double scale=10.;
       if(s[m][i]>=1)    int iterscale=0;
         mw[++mi][i]=m;  
       if(m >=lastpass)    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
         break;    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
       else  
         m++;  
     }/* end while */    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
     if (s[m][i] > nlstate){    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
       mi++;     /* Death is another wave */    /*   *bx = *ax - (*ax - *bx)/scale; */
       /* if(mi==0)  never been interviewed correctly before death */    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
          /* Only death is a correct wave */    /* } */
       mw[mi][i]=m;  
     }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
     wav[i]=mi;      SHFT(dum,*fb,*fa,dum) 
     if(mi==0)    } 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    *cx=(*bx)+GOLD*(*bx-*ax); 
   }    *fc=(*func)(*cx); 
   #ifdef DEBUG
   for(i=1; i<=imx; i++){    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
     for(mi=1; mi<wav[i];mi++){    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
       if (stepm <=0)  #endif
         dh[mi][i]=1;    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
       else{      r=(*bx-*ax)*(*fb-*fc); 
         if (s[mw[mi+1][i]][i] > nlstate) {      q=(*bx-*cx)*(*fb-*fa); 
           if (agedc[i] < 2*AGESUP) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
           if(j==0) j=1;  /* Survives at least one month after exam */      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
           k=k+1;      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
           if (j >= jmax) jmax=j;        fu=(*func)(u); 
           if (j <= jmin) jmin=j;  #ifdef DEBUG
           sum=sum+j;        /* f(x)=A(x-u)**2+f(u) */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        double A, fparabu; 
           }        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         }        fparabu= *fa - A*(*ax-u)*(*ax-u);
         else{        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);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        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);
           k=k+1;        /* And thus,it can be that fu > *fc even if fparabu < *fc */
           if (j >= jmax) jmax=j;        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
           else if (j <= jmin)jmin=j;          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
           sum=sum+j;  #endif 
         }  #ifdef MNBRAKORIGINAL
         jk= j/stepm;  #else
         jl= j -jk*stepm;  /*       if (fu > *fc) { */
         ju= j -(jk+1)*stepm;  /* #ifdef DEBUG */
         if(jl <= -ju)  /*       printf("mnbrak4  fu > fc \n"); */
           dh[mi][i]=jk;  /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
         else  /* #endif */
           dh[mi][i]=jk+1;  /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
         if(dh[mi][i]==0)  /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
           dh[mi][i]=1; /* At least one step */  /*      dum=u; /\* Shifting c and u *\/ */
       }  /*      u = *cx; */
     }  /*      *cx = dum; */
   }  /*      dum = fu; */
   jmean=sum/k;  /*      fu = *fc; */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  /*      *fc =dum; */
  }  /*       } else { /\* end *\/ */
 /*********** Tricode ****************************/  /* #ifdef DEBUG */
 void tricode(int *Tvar, int **nbcode, int imx)  /*       printf("mnbrak3  fu < fc \n"); */
 {  /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
   int Ndum[20],ij=1, k, j, i;  /* #endif */
   int cptcode=0;  /*      dum=u; /\* Shifting c and u *\/ */
   cptcoveff=0;  /*      u = *cx; */
    /*      *cx = dum; */
   for (k=0; k<19; k++) Ndum[k]=0;  /*      dum = fu; */
   for (k=1; k<=7; k++) ncodemax[k]=0;  /*      fu = *fc; */
   /*      *fc =dum; */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  /*       } */
     for (i=1; i<=imx; i++) {  #ifdef DEBUG
       ij=(int)(covar[Tvar[j]][i]);        printf("mnbrak34  fu < or >= fc \n");
       Ndum[ij]++;        fprintf(ficlog, "mnbrak34 fu < fc\n");
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  #endif
       if (ij > cptcode) cptcode=ij;        dum=u; /* Shifting c and u */
     }        u = *cx;
         *cx = dum;
     for (i=0; i<=cptcode; i++) {        dum = fu;
       if(Ndum[i]!=0) ncodemax[j]++;        fu = *fc;
     }        *fc =dum;
     ij=1;  #endif
       } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   #ifdef DEBUG
     for (i=1; i<=ncodemax[j]; i++) {        printf("mnbrak2  u after c but before ulim\n");
       for (k=0; k<=19; k++) {        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
         if (Ndum[k] != 0) {  #endif
           nbcode[Tvar[j]][ij]=k;        fu=(*func)(u); 
                  if (fu < *fc) { 
           ij++;  #ifdef DEBUG
         }        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
         if (ij > ncodemax[j]) break;        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
       }    #endif
     }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   }            SHFT(*fb,*fc,fu,(*func)(u)) 
         } 
  for (k=0; k<19; k++) Ndum[k]=0;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   #ifdef DEBUG
  for (i=1; i<=ncovmodel-2; i++) {        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
       ij=Tvar[i];        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
       Ndum[ij]++;  #endif
     }        u=ulim; 
         fu=(*func)(u); 
  ij=1;      } else { /* u could be left to b (if r > q parabola has a maximum) */
  for (i=1; i<=10; i++) {  #ifdef DEBUG
    if((Ndum[i]!=0) && (i<=ncovcol)){        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
      Tvaraff[ij]=i;        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
      ij++;  #endif
    }        u=(*cx)+GOLD*(*cx-*bx); 
  }        fu=(*func)(u); 
        } /* end tests */
     cptcoveff=ij-1;      SHFT(*ax,*bx,*cx,u) 
 }      SHFT(*fa,*fb,*fc,fu) 
   #ifdef DEBUG
 /*********** Health Expectancies ****************/        printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
         fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
 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 )  #endif
     } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
 {  } 
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  /*************** linmin ************************/
   double age, agelim, hf;  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
   double ***p3mat,***varhe;  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   double **dnewm,**doldm;  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
   double *xp;  the value of func at the returned location p . This is actually all accomplished by calling the
   double **gp, **gm;  routines mnbrak and brent .*/
   double ***gradg, ***trgradg;  int ncom; 
   int theta;  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);   
   xp=vector(1,npar);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   dnewm=matrix(1,nlstate*2,1,npar);  { 
   doldm=matrix(1,nlstate*2,1,nlstate*2);    double brent(double ax, double bx, double cx, 
                   double (*f)(double), double tol, double *xmin); 
   fprintf(ficreseij,"# Health expectancies\n");    double f1dim(double x); 
   fprintf(ficreseij,"# Age");    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   for(i=1; i<=nlstate;i++)                double *fc, double (*func)(double)); 
     for(j=1; j<=nlstate;j++)    int j; 
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    double xx,xmin,bx,ax; 
   fprintf(ficreseij,"\n");    double fx,fb,fa;
   
   if(estepm < stepm){    double scale=10., axs, xxs, xxss; /* Scale added for infinity */
     printf ("Problem %d lower than %d\n",estepm, stepm);   
   }    ncom=n; 
   else  hstepm=estepm;      pcom=vector(1,n); 
   /* We compute the life expectancy from trapezoids spaced every estepm months    xicom=vector(1,n); 
    * This is mainly to measure the difference between two models: for example    nrfunc=func; 
    * if stepm=24 months pijx are given only every 2 years and by summing them    for (j=1;j<=n;j++) { 
    * we are calculating an estimate of the Life Expectancy assuming a linear      pcom[j]=p[j]; 
    * progression inbetween and thus overestimating or underestimating according      xicom[j]=xi[j]; 
    * to the curvature of the survival function. If, for the same date, we    } 
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  
    * to compare the new estimate of Life expectancy with the same linear    /* axs=0.0; */
    * hypothesis. A more precise result, taking into account a more precise    /* xxss=1; /\* 1 and using scale *\/ */
    * curvature will be obtained if estepm is as small as stepm. */    xxs=1;
     /* do{ */
   /* For example we decided to compute the life expectancy with the smallest unit */      ax=0.;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      xx= xxs;
      nhstepm is the number of hstepm from age to agelim      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
      nstepm is the number of stepm from age to agelin.      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
      Look at hpijx to understand the reason of that which relies in memory size      /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
      and note for a fixed period like estepm months */      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
      survival function given by stepm (the optimization length). Unfortunately it      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
      means that if the survival funtion is printed only each two years of age and if      /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    /*   if (fx != fx){ */
      results. So we changed our mind and took the option of the best precision.    /*    xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
   */    /*    printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    /*   } */
     /* }while(fx != fx); */
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #ifdef DEBUGLINMIN
     /* nhstepm age range expressed in number of stepm */    printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  #endif
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
     /* if (stepm >= YEARM) hstepm=1;*/    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    /* fmin = f(p[j] + xmin * xi[j]) */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
     gp=matrix(0,nhstepm,1,nlstate*2);  #ifdef DEBUG
     gm=matrix(0,nhstepm,1,nlstate*2);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  #endif
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  #ifdef DEBUGLINMIN
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      printf("linmin end ");
    #endif
     for (j=1;j<=n;j++) { 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
       xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
     /* Computing Variances of health expectancies */      /* if(xxs <1.0) */
       /*   printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */
      for(theta=1; theta <=npar; theta++){      p[j] += xi[j]; /* Parameters values are updated accordingly */
       for(i=1; i<=npar; i++){    } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* printf("\n"); */
       }  #ifdef DEBUGLINMIN
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
      for (j=1;j<=n;j++) { 
       cptj=0;      printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
       for(j=1; j<= nlstate; j++){      if(j % ncovmodel == 0)
         for(i=1; i<=nlstate; i++){        printf("\n");
           cptj=cptj+1;    }
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  #endif
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    free_vector(xicom,1,n); 
           }    free_vector(pcom,1,n); 
         }  } 
       }  
        
        /*************** powell ************************/
       for(i=1; i<=npar; i++)  /*
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  Minimization of a function func of n variables. Input consists of an initial starting point
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
        rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
       cptj=0;  such that failure to decrease by more than this amount on one iteration signals doneness. On
       for(j=1; j<= nlstate; j++){  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
         for(i=1;i<=nlstate;i++){  function value at p , and iter is the number of iterations taken. The routine linmin is used.
           cptj=cptj+1;   */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;              double (*func)(double [])) 
           }  { 
         }    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
          int i,ibig,j; 
        double del,t,*pt,*ptt,*xit;
     double directest;
       for(j=1; j<= nlstate*2; j++)    double fp,fptt;
         for(h=0; h<=nhstepm-1; h++){    double *xits;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    int niterf, itmp;
         }  
     pt=vector(1,n); 
      }    ptt=vector(1,n); 
        xit=vector(1,n); 
 /* End theta */    xits=vector(1,n); 
     *fret=(*func)(p); 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    for (j=1;j<=n;j++) pt[j]=p[j]; 
       rcurr_time = time(NULL);  
      for(h=0; h<=nhstepm-1; h++)    for (*iter=1;;++(*iter)) { 
       for(j=1; j<=nlstate*2;j++)      fp=(*fret); /* From former iteration or initial value */
         for(theta=1; theta <=npar; theta++)      ibig=0; 
         trgradg[h][j][theta]=gradg[h][theta][j];      del=0.0; 
       rlast_time=rcurr_time;
       /* (void) gettimeofday(&curr_time,&tzp); */
      for(i=1;i<=nlstate*2;i++)      rcurr_time = time(NULL);  
       for(j=1;j<=nlstate*2;j++)      curr_time = *localtime(&rcurr_time);
         varhe[i][j][(int)age] =0.;      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);
      printf("%d|",(int)age);fflush(stdout);  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
     for(h=0;h<=nhstepm-1;h++){      for (i=1;i<=n;i++) {
       for(k=0;k<=nhstepm-1;k++){        printf(" %d %.12f",i, p[i]);
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        fprintf(ficlog," %d %.12lf",i, p[i]);
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        fprintf(ficrespow," %.12lf", p[i]);
         for(i=1;i<=nlstate*2;i++)      }
           for(j=1;j<=nlstate*2;j++)      printf("\n");
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;      fprintf(ficlog,"\n");
       }      fprintf(ficrespow,"\n");fflush(ficrespow);
     }      if(*iter <=3){
         tml = *localtime(&rcurr_time);
              strcpy(strcurr,asctime(&tml));
     /* Computing expectancies */        rforecast_time=rcurr_time; 
     for(i=1; i<=nlstate;i++)        itmp = strlen(strcurr);
       for(j=1; j<=nlstate;j++)        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          strcurr[itmp-1]='\0';
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
                  fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
 /* 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(niterf=10;niterf<=30;niterf+=10){
           rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         }          forecast_time = *localtime(&rforecast_time);
           strcpy(strfor,asctime(&forecast_time));
     fprintf(ficreseij,"%3.0f",age );          itmp = strlen(strfor);
     cptj=0;          if(strfor[itmp-1]=='\n')
     for(i=1; i<=nlstate;i++)          strfor[itmp-1]='\0';
       for(j=1; j<=nlstate;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);
         cptj++;          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);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        }
       }      }
     fprintf(ficreseij,"\n");      for (i=1;i<=n;i++) { /* For each direction i */
            for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
     free_matrix(gm,0,nhstepm,1,nlstate*2);        fptt=(*fret); 
     free_matrix(gp,0,nhstepm,1,nlstate*2);  #ifdef DEBUG
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #endif
   }            printf("%d",i);fflush(stdout); /* print direction (parameter) i */
   free_vector(xp,1,npar);        fprintf(ficlog,"%d",i);fflush(ficlog);
   free_matrix(dnewm,1,nlstate*2,1,npar);        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);                                      /* Outputs are fret(new point p) p is updated and xit rescaled */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        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 */
           /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
 /************ Variance ******************/          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
 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)          /* with the new direction. */
 {          del=fabs(fptt-(*fret)); 
   /* Variance of health expectancies */          ibig=i; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        } 
   double **newm;  #ifdef DEBUG
   double **dnewm,**doldm;        printf("%d %.12e",i,(*fret));
   int i, j, nhstepm, hstepm, h, nstepm ;        fprintf(ficlog,"%d %.12e",i,(*fret));
   int k, cptcode;        for (j=1;j<=n;j++) {
   double *xp;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double **gp, **gm;          printf(" x(%d)=%.12e",j,xit[j]);
   double ***gradg, ***trgradg;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double ***p3mat;        }
   double age,agelim, hf;        for(j=1;j<=n;j++) {
   int theta;          printf(" p(%d)=%.12e",j,p[j]);
           fprintf(ficlog," p(%d)=%.12e",j,p[j]);
   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");        }
   fprintf(ficresvij,"# Age");        printf("\n");
   for(i=1; i<=nlstate;i++)        fprintf(ficlog,"\n");
     for(j=1; j<=nlstate;j++)  #endif
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      } /* end loop on each direction i */
   fprintf(ficresvij,"\n");      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
       /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
   xp=vector(1,npar);      /* New value of last point Pn is not computed, P(n-1) */
   dnewm=matrix(1,nlstate,1,npar);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
   doldm=matrix(1,nlstate,1,nlstate);        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
          /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
   if(estepm < stepm){        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
     printf ("Problem %d lower than %d\n",estepm, stepm);        /* decreased of more than 3.84  */
   }        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
   else  hstepm=estepm;          /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
   /* For example we decided to compute the life expectancy with the smallest unit */        /* By adding 10 parameters more the gain should be 18.31 */
   /* 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        /* Starting the program with initial values given by a former maximization will simply change */
      nstepm is the number of stepm from age to agelin.        /* the scales of the directions and the directions, because the are reset to canonical directions */
      Look at hpijx to understand the reason of that which relies in memory size        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
      and note for a fixed period like k years */        /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  #ifdef DEBUG
      survival function given by stepm (the optimization length). Unfortunately it        int k[2],l;
      means that if the survival funtion is printed only each two years of age and if        k[0]=1;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        k[1]=-1;
      results. So we changed our mind and took the option of the best precision.        printf("Max: %.12e",(*func)(p));
   */        fprintf(ficlog,"Max: %.12e",(*func)(p));
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        for (j=1;j<=n;j++) {
   agelim = AGESUP;          printf(" %.12e",p[j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          fprintf(ficlog," %.12e",p[j]);
     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 */        printf("\n");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficlog,"\n");
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        for(l=0;l<=1;l++) {
     gp=matrix(0,nhstepm,1,nlstate);          for (j=1;j<=n;j++) {
     gm=matrix(0,nhstepm,1,nlstate);            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]);
     for(theta=1; theta <=npar; theta++){            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<=npar; i++){ /* Computes gradient */          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  #endif
   
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)        free_vector(xit,1,n); 
           prlim[i][i]=probs[(int)age][i][ij];        free_vector(xits,1,n); 
       }        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
       for(j=1; j<= nlstate; j++){        return; 
         for(h=0; h<=nhstepm; h++){      } /* enough precision */ 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      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]; 
       }        xit[j]=p[j]-pt[j]; 
            pt[j]=p[j]; 
       for(i=1; i<=npar; i++) /* Computes gradient */      } 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      fptt=(*func)(ptt); /* f_3 */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #ifdef POWELLF1F3
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  #else
        if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
       if (popbased==1) {  #endif
         for(i=1; i<=nlstate;i++)        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
           prlim[i][i]=probs[(int)age][i][ij];        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
       }        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
         /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
       for(j=1; j<= nlstate; j++){        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         for(h=0; h<=nhstepm; h++){        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  #ifdef NRCORIGINAL
         }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
       }  #else
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       for(j=1; j<= nlstate; j++)        t= t- del*SQR(fp-fptt);
         for(h=0; h<=nhstepm; h++){  #endif
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
         }  #ifdef DEBUG
     } /* End theta */        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);
         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);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     for(h=0; h<=nhstepm; h++)        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       for(j=1; j<=nlstate;j++)               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         for(theta=1; theta <=npar; theta++)        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);
           trgradg[h][j][theta]=gradg[h][theta][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);
   #endif
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  #ifdef POWELLORIGINAL
     for(i=1;i<=nlstate;i++)        if (t < 0.0) { /* Then we use it for new direction */
       for(j=1;j<=nlstate;j++)  #else
         vareij[i][j][(int)age] =0.;        if (directest*t < 0.0) { /* Contradiction between both tests */
           printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
     for(h=0;h<=nhstepm;h++){          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       for(k=0;k<=nhstepm;k++){          fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        } 
         for(i=1;i<=nlstate;i++)        if (directest < 0.0) { /* Then we use it for new direction */
           for(j=1;j<=nlstate;j++)  #endif
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  #ifdef DEBUGLINMIN
       }          printf("Before linmin in direction P%d-P0\n",n);
     }          for (j=1;j<=n;j++) { 
             printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
     fprintf(ficresvij,"%.0f ",age );            if(j % ncovmodel == 0)
     for(i=1; i<=nlstate;i++)              printf("\n");
       for(j=1; j<=nlstate;j++){          }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  #endif
       }          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
     fprintf(ficresvij,"\n");  #ifdef DEBUGLINMIN
     free_matrix(gp,0,nhstepm,1,nlstate);          for (j=1;j<=n;j++) { 
     free_matrix(gm,0,nhstepm,1,nlstate);            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            if(j % ncovmodel == 0)
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);              printf("\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   } /* End age */  #endif
            for (j=1;j<=n;j++) { 
   free_vector(xp,1,npar);            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
   free_matrix(doldm,1,nlstate,1,npar);            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
   free_matrix(dnewm,1,nlstate,1,nlstate);          }
           printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
 }          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   
 /************ Variance of prevlim ******************/  #ifdef DEBUG
 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)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   /* Variance of prevalence limit */          for(j=1;j<=n;j++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            printf(" %.12e",xit[j]);
   double **newm;            fprintf(ficlog," %.12e",xit[j]);
   double **dnewm,**doldm;          }
   int i, j, nhstepm, hstepm;          printf("\n");
   int k, cptcode;          fprintf(ficlog,"\n");
   double *xp;  #endif
   double *gp, *gm;        } /* end of t or directest negative */
   double **gradg, **trgradg;  #ifdef POWELLF1F3
   double age,agelim;  #else
   int theta;      } /* end if (fptt < fp)  */
      #endif
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    } /* loop iteration */ 
   fprintf(ficresvpl,"# Age");  } 
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);  /**** Prevalence limit (stable or period prevalence)  ****************/
   fprintf(ficresvpl,"\n");  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   xp=vector(1,npar);  {
   dnewm=matrix(1,nlstate,1,npar);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   doldm=matrix(1,nlstate,1,nlstate);       matrix by transitions matrix until convergence is reached */
      
   hstepm=1*YEARM; /* Every year of age */    int i, ii,j,k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double min, max, maxmin, maxmax,sumnew=0.;
   agelim = AGESUP;    /* double **matprod2(); */ /* test */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double **out, cov[NCOVMAX+1], **pmij();
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double **newm;
     if (stepm >= YEARM) hstepm=1;    double agefin, delaymax=50 ; /* Max number of years to converge */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    
     gradg=matrix(1,npar,1,nlstate);    for (ii=1;ii<=nlstate+ndeath;ii++)
     gp=vector(1,nlstate);      for (j=1;j<=nlstate+ndeath;j++){
     gm=vector(1,nlstate);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
     for(theta=1; theta <=npar; theta++){    
       for(i=1; i<=npar; i++){ /* Computes gradient */    cov[1]=1.;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    
       }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       for(i=1;i<=nlstate;i++)      newm=savm;
         gp[i] = prlim[i][i];      /* Covariates have to be included here again */
          cov[2]=agefin;
       for(i=1; i<=npar; i++) /* Computes gradient */      if(nagesqr==1)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        cov[3]= agefin*agefin;;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (k=1; k<=cptcovn;k++) {
       for(i=1;i<=nlstate;i++)        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         gm[i] = prlim[i][i];        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
       }
       for(i=1;i<=nlstate;i++)      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
     } /* End theta */      for (k=1; k<=cptcovprod;k++) /* Useless */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     trgradg =matrix(1,nlstate,1,npar);      
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for(j=1; j<=nlstate;j++)      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       for(theta=1; theta <=npar; theta++)      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         trgradg[j][theta]=gradg[theta][j];      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       /* 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 */
       varpl[i][(int)age] =0.;      
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      savm=oldm;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      oldm=newm;
     for(i=1;i<=nlstate;i++)      maxmax=0.;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      for(j=1;j<=nlstate;j++){
         min=1.;
     fprintf(ficresvpl,"%.0f ",age );        max=0.;
     for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate; i++) {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          sumnew=0;
     fprintf(ficresvpl,"\n");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     free_vector(gp,1,nlstate);          prlim[i][j]= newm[i][j]/(1-sumnew);
     free_vector(gm,1,nlstate);          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
     free_matrix(gradg,1,npar,1,nlstate);          max=FMAX(max,prlim[i][j]);
     free_matrix(trgradg,1,nlstate,1,npar);          min=FMIN(min,prlim[i][j]);
   } /* End age */        }
         maxmin=max-min;
   free_vector(xp,1,npar);        maxmax=FMAX(maxmax,maxmin);
   free_matrix(doldm,1,nlstate,1,npar);      } /* j loop */
   free_matrix(dnewm,1,nlstate,1,nlstate);      if(maxmax < ftolpl){
         return prlim;
 }      }
     } /* age loop */
 /************ Variance of one-step probabilities  ******************/    return prlim; /* should not reach here */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  }
 {  
   int i, j, i1, k1, j1, z1;  /*************** transition probabilities ***************/ 
   int k=0, cptcode;  
   double **dnewm,**doldm;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   double *xp;  {
   double *gp, *gm;    /* According to parameters values stored in x and the covariate's values stored in cov,
   double **gradg, **trgradg;       computes the probability to be observed in state j being in state i by appying the
   double age,agelim, cov[NCOVMAX];       model to the ncovmodel covariates (including constant and age).
   int theta;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   char fileresprob[FILENAMELENGTH];       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
   strcpy(fileresprob,"prob");       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   strcat(fileresprob,fileres);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     printf("Problem with resultfile: %s\n", fileresprob);       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
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
      */
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    double s1, lnpijopii;
   fprintf(ficresprob,"# Age");    /*double t34;*/
   for(i=1; i<=nlstate;i++)    int i,j, nc, ii, jj;
     for(j=1; j<=(nlstate+ndeath);j++)  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   fprintf(ficresprob,"\n");            /*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); */
   xp=vector(1,npar);          }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
          }
   cov[1]=1;        for(j=i+1; j<=nlstate+ndeath;j++){
   j=cptcoveff;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   j1=0;            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   for(k1=1; k1<=1;k1++){  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     for(i1=1; i1<=ncodemax[k1];i1++){          }
     j1++;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }
     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]]);      for(i=1; i<= nlstate; i++){
       fprintf(ficresprob, "**********\n#");        s1=0;
     }        for(j=1; j<i; j++){
              s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       for (age=bage; age<=fage; age ++){          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         cov[2]=age;        }
         for (k=1; k<=cptcovn;k++) {        for(j=i+1; j<=nlstate+ndeath; j++){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                    /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }        }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         for (k=1; k<=cptcovprod;k++)        ps[i][i]=1./(s1+1.);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        /* Computing other pijs */
                for(j=1; j<i; j++)
         gradg=matrix(1,npar,1,9);          ps[i][j]= exp(ps[i][j])*ps[i][i];
         trgradg=matrix(1,9,1,npar);        for(j=i+1; j<=nlstate+ndeath; j++)
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          ps[i][j]= exp(ps[i][j])*ps[i][i];
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
          } /* end i */
         for(theta=1; theta <=npar; theta++){      
           for(i=1; i<=npar; i++)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(jj=1; jj<= nlstate+ndeath; jj++){
                    ps[ii][jj]=0;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          ps[ii][ii]=1;
                  }
           k=0;      }
           for(i=1; i<= (nlstate+ndeath); i++){      
             for(j=1; j<=(nlstate+ndeath);j++){      
               k=k+1;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
               gp[k]=pmmij[i][j];      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
             }      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
           }      /*   } */
                /*   printf("\n "); */
           for(i=1; i<=npar; i++)      /* } */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      /* printf("\n ");printf("%lf ",cov[2]);*/
          /*
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           k=0;        goto end;*/
           for(i=1; i<=(nlstate+ndeath); i++){      return ps;
             for(j=1; j<=(nlstate+ndeath);j++){  }
               k=k+1;  
               gm[k]=pmmij[i][j];  /**************** Product of 2 matrices ******************/
             }  
           }  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
        {
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];         b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         }    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)       a pointer to pointers identical to out */
           for(theta=1; theta <=npar; theta++)    int i, j, k;
             trgradg[j][theta]=gradg[theta][j];    for(i=nrl; i<= nrh; i++)
              for(k=ncolol; k<=ncoloh; k++){
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        out[i][k]=0.;
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        for(j=ncl; j<=nch; j++)
                  out[i][k] +=in[i][j]*b[j][k];
         pmij(pmmij,cov,ncovmodel,x,nlstate);      }
            return out;
         k=0;  }
         for(i=1; i<=(nlstate+ndeath); i++){  
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;  /************* Higher Matrix Product ***************/
             gm[k]=pmmij[i][j];  
           }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         }  {
          /* Computes the transition matrix starting at age 'age' over 
      /*printf("\n%d ",(int)age);       'nhstepm*hstepm*stepm' months (i.e. until
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));       nhstepm*hstepm matrices. 
      }*/       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 
         fprintf(ficresprob,"\n%d ",(int)age);       for the memory).
        Model is determined by parameters x and covariates have to be 
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)       included manually here. 
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));  
         */
       }  
     }    int i, j, d, h, k;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double **out, cov[NCOVMAX+1];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double **newm;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double agexact;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }    /* Hstepm could be zero and should return the unit matrix */
   free_vector(xp,1,npar);    for (i=1;i<=nlstate+ndeath;i++)
   fclose(ficresprob);      for (j=1;j<=nlstate+ndeath;j++){
          oldm[i][j]=(i==j ? 1.0 : 0.0);
 }        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 /******************* Printing html file ***********/    for(h=1; h <=nhstepm; h++){
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      for(d=1; d <=hstepm; d++){
                   int lastpass, int stepm, int weightopt, char model[],\        newm=savm;
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \        /* Covariates have to be included here again */
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\        cov[1]=1.;
                   char version[], int popforecast, int estepm ,\        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
                   double jprev1, double mprev1,double anprev1, \        cov[2]=agexact;
                   double jprev2, double mprev2,double anprev2){        if(nagesqr==1)
   int jj1, k1, i1, cpt;          cov[3]= agexact*agexact;
   FILE *fichtm;        for (k=1; k<=cptcovn;k++) 
   /*char optionfilehtm[FILENAMELENGTH];*/          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
   strcpy(optionfilehtm,optionfile);          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   strcat(optionfilehtm,".htm");          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
     printf("Problem with %s \n",optionfilehtm), exit(0);          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }  
   
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 \n        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 Total number of observations=%d <br>\n                     pmij(pmmij,cov,ncovmodel,x,nlstate));
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        savm=oldm;
 <hr  size=\"2\" color=\"#EC5E5E\">        oldm=newm;
  <ul><li>Parameter files<br>\n      }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      for(i=1; i<=nlstate+ndeath; i++)
  - 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);        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
  - 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        }
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n      /*printf("h=%d ",h);*/
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    } /* end h */
  - Life expectancies by age and initial health status (estepm=%2d months):  /*     printf("\n H=%d \n",h); */
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    return po;
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  }
   
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n  #ifdef NLOPT
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    double fret;
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    double *xt;
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    int j;
  - 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);    myfunc_data *d2 = (myfunc_data *) pd;
   /* xt = (p1-1); */
  if(popforecast==1) fprintf(fichtm,"\n    xt=vector(1,n); 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
  else    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
    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);    printf("Function = %.12lf ",fret);
 fprintf(fichtm," <li>Graphs</li><p>");    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf("\n");
  m=cptcoveff;   free_vector(xt,1,n);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    return fret;
   }
  jj1=0;  #endif
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  /*************** log-likelihood *************/
      jj1++;  double func( double *x)
      if (cptcovn > 0) {  {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    int i, ii, j, k, mi, d, kk;
        for (cpt=1; cpt<=cptcoveff;cpt++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double **out;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double sw; /* Sum of weights */
      }    double lli; /* Individual log likelihood */
      /* Pij */    int s1, s2;
      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>    double bbh, survp;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        long ipmx;
      /* Quasi-incidences */    double agexact;
      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>    /*extern weight */
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    /* We are differentiating ll according to initial status */
        /* Stable prevalence in each health state */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        for(cpt=1; cpt<nlstate;cpt++){    /*for(i=1;i<imx;i++) 
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>      printf(" %d\n",s[4][i]);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    */
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {    ++countcallfunc;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.png <br>    cov[1]=1.;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }    for(k=1; k<=nlstate; k++) ll[k]=0.;
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    if(mle==1){
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      }        /* Computes the values of the ncovmodel covariates of the model
      fprintf(fichtm,"\n<br>- Total life expectancy by age and           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
 health expectancies in states (1) and (2): e%s%d.png<br>           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);           to be observed in j being in i according to the model.
 fprintf(fichtm,"\n</body>");         */
    }        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
  }            cov[2+nagesqr+k]=covar[Tvar[k]][i];
 fclose(fichtm);        }
 }        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
 /******************* Gnuplot file **************/           has been calculated etc */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            for (j=1;j<=nlstate+ndeath;j++){
   int ng;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcpy(optionfilegnuplot,optionfilefiname);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(optionfilegnuplot,".gp.txt");            }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          for(d=0; d<dh[mi][i]; d++){
     printf("Problem with file %s",optionfilegnuplot);            newm=savm;
   }            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
 #ifdef windows            if(nagesqr==1)
     fprintf(ficgp,"cd \"%s\" \n",pathc);              cov[3]= agexact*agexact;
 #endif            for (kk=1; kk<=cptcovage;kk++) {
 m=pow(2,cptcoveff);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
              }
  /* 1eme*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (cpt=1; cpt<= nlstate ; cpt ++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    for (k1=1; k1<= m ; k1 ++) {            savm=oldm;
             oldm=newm;
 #ifdef windows          } /* end mult */
      fprintf(ficgp,"\nset out \"v%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] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 #endif          /* But now since version 0.9 we anticipate for bias at large stepm.
 #ifdef unix           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);           * (in months) between two waves is not a multiple of stepm, we rounded to 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);           * the nearest (and in case of equal distance, to the lowest) interval but now
 #endif           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 for (i=1; i<= nlstate ; i ++) {           * probability in order to take into account the bias as a fraction of the way
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   else fprintf(ficgp," \%%*lf (\%%*lf)");           * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);           * For stepm > 1 the results are less biased than in previous versions. 
     for (i=1; i<= nlstate ; i ++) {           */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          s1=s[mw[mi][i]][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          /* bias bh is positive if real duration
      for (i=1; i<= nlstate ; i ++) {           * is higher than the multiple of stepm and negative otherwise.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 }            if( s2 > nlstate){ 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            /* i.e. if s2 is a death state and if the date of death is known 
 #ifdef unix               then the contribution to the likelihood is the probability to 
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");               die between last step unit time and current  step unit time, 
 #endif               which is also equal to probability to die before dh 
    }               minus probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
   /*2 eme*/          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
   for (k1=1; k1<= m ; k1 ++) {          and not the date of a change in health state. The former idea was
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          to consider that at each interview the state was recorded
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          (healthy, disable or death) and IMaCh was corrected; but when we
              introduced the exact date of death then we should have modified
     for (i=1; i<= nlstate+1 ; i ++) {          the contribution of an exact death to the likelihood. This new
       k=2*i;          contribution is smaller and very dependent of the step unit
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          stepm. It is no more the probability to die between last interview
       for (j=1; j<= nlstate+1 ; j ++) {          and month of death but the probability to survive from last
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          interview up to one month before death multiplied by the
   else fprintf(ficgp," \%%*lf (\%%*lf)");          probability to die within a month. Thanks to Chris
 }            Jackson for correcting this bug.  Former versions increased
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          mortality artificially. The bad side is that we add another loop
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          which slows down the processing. The difference can be up to 10%
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          lower mortality.
       for (j=1; j<= nlstate+1 ; j ++) {            */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          /* If, at the beginning of the maximization mostly, the
         else fprintf(ficgp," \%%*lf (\%%*lf)");             cumulative probability or probability to be dead is
 }               constant (ie = 1) over time d, the difference is equal to
       fprintf(ficgp,"\" t\"\" w l 0,");             0.  out[s1][3] = savm[s1][3]: probability, being at state
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);             s1 at precedent wave, to be dead a month before current
       for (j=1; j<= nlstate+1 ; j ++) {             wave is equal to probability, being at state s1 at
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");             precedent wave, to be dead at mont of the current
   else fprintf(ficgp," \%%*lf (\%%*lf)");             wave. Then the observed probability (that this person died)
 }               is null according to current estimated parameter. In fact,
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");             it should be very low but not zero otherwise the log go to
       else fprintf(ficgp,"\" t\"\" w l 0,");             infinity.
     }          */
   }  /* #ifdef INFINITYORIGINAL */
    /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /*3eme*/  /* #else */
   /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
   for (k1=1; k1<= m ; k1 ++) {  /*          lli=log(mytinydouble); */
     for (cpt=1; cpt<= nlstate ; cpt ++) {  /*        else */
       k=2+nlstate*(2*cpt-2);  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  /* #endif */
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);              lli=log(out[s1][s2] - savm[s1][s2]);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          } else if  (s2==-2) {
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            for (j=1,survp=0. ; j<=nlstate; j++) 
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            /*survp += out[s1][j]; */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            lli= log(survp);
           }
 */          
       for (i=1; i< nlstate ; i ++) {          else if  (s2==-4) { 
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);            for (j=3,survp=0. ; j<=nlstate; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
     }          } 
   }  
            else if  (s2==-5) { 
   /* CV preval stat */            for (j=1,survp=0. ; j<=2; j++)  
     for (k1=1; k1<= m ; k1 ++) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for (cpt=1; cpt<nlstate ; cpt ++) {            lli= log(survp); 
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for (i=1; i< nlstate ; i ++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         fprintf(ficgp,"+$%d",k+i+1);          } 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                /*if(lli ==000.0)*/
       l=3+(nlstate+ndeath)*cpt;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          ipmx +=1;
       for (i=1; i< nlstate ; i ++) {          sw += weight[i];
         l=3+(nlstate+ndeath)*cpt;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficgp,"+$%d",l+i+1);          /* if (lli < log(mytinydouble)){ */
       }          /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
     }          /* } */
   }          } /* end of wave */
        } /* end of individual */
   /* proba elementaires */    }  else if(mle==2){
    for(i=1,jk=1; i <=nlstate; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(k=1; k <=(nlstate+ndeath); k++){        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       if (k != i) {        for(mi=1; mi<= wav[i]-1; mi++){
         for(j=1; j <=ncovmodel; j++){          for (ii=1;ii<=nlstate+ndeath;ii++)
                    for (j=1;j<=nlstate+ndeath;j++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           jk++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           fprintf(ficgp,"\n");            }
         }          for(d=0; d<=dh[mi][i]; d++){
       }            newm=savm;
     }            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
    }            cov[2]=agexact;
             if(nagesqr==1)
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/              cov[3]= agexact*agexact;
      for(jk=1; jk <=m; jk++) {            for (kk=1; kk<=cptcovage;kk++) {
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
        if (ng==2)            }
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
        else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          fprintf(ficgp,"\nset title \"Probability\"\n");            savm=oldm;
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            oldm=newm;
        i=1;          } /* end mult */
        for(k2=1; k2<=nlstate; k2++) {        
          k3=i;          s1=s[mw[mi][i]][i];
          for(k=1; k<=(nlstate+ndeath); k++) {          s2=s[mw[mi+1][i]][i];
            if (k != k2){          bbh=(double)bh[mi][i]/(double)stepm; 
              if(ng==2)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
                fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+1);          ipmx +=1;
              else          sw += weight[i];
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
              ij=1;        } /* end of wave */
              for(j=3; j <=ncovmodel; j++) {      } /* end of individual */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    }  else if(mle==3){  /* exponential inter-extrapolation */
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                  ij++;        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                }        for(mi=1; mi<= wav[i]-1; mi++){
                else          for (ii=1;ii<=nlstate+ndeath;ii++)
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            for (j=1;j<=nlstate+ndeath;j++){
              }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              fprintf(ficgp,")/(1");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                          }
              for(k1=1; k1 <=nlstate; k1++){            for(d=0; d<dh[mi][i]; d++){
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            newm=savm;
                ij=1;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for(j=3; j <=ncovmodel; j++){            cov[2]=agexact;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            if(nagesqr==1)
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              cov[3]= agexact*agexact;
                    ij++;            for (kk=1; kk<=cptcovage;kk++) {
                  }              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                  else            }
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                fprintf(ficgp,")");            savm=oldm;
              }            oldm=newm;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);          } /* end mult */
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        
              i=i+ncovmodel;          s1=s[mw[mi][i]][i];
            }          s2=s[mw[mi+1][i]][i];
          }          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 */
      }          ipmx +=1;
    }          sw += weight[i];
    fclose(ficgp);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 }  /* end gnuplot */        } /* end of wave */
       } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
 /*************** Moving average **************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   int i, cpt, cptcod;          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)            for (j=1;j<=nlstate+ndeath;j++){
       for (i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           mobaverage[(int)agedeb][i][cptcod]=0.;            }
              for(d=0; d<dh[mi][i]; d++){
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){            newm=savm;
       for (i=1; i<=nlstate;i++){            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            cov[2]=agexact;
           for (cpt=0;cpt<=4;cpt++){            if(nagesqr==1)
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              cov[3]= agexact*agexact;
           }            for (kk=1; kk<=cptcovage;kk++) {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
         }            }
       }          
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
           } /* end mult */
 /************** 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){          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          if( s2 > nlstate){ 
   int *popage;            lli=log(out[s1][s2] - savm[s1][s2]);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          }else{
   double *popeffectif,*popcount;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double ***p3mat;          }
   char fileresf[FILENAMELENGTH];          ipmx +=1;
           sw += weight[i];
  agelim=AGESUP;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      } /* end of individual */
      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcpy(fileresf,"f");        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   strcat(fileresf,fileres);        for(mi=1; mi<= wav[i]-1; mi++){
   if((ficresf=fopen(fileresf,"w"))==NULL) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("Problem with forecast resultfile: %s\n", fileresf);            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("Computing forecasting: result on file '%s' \n", fileresf);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   if (mobilav==1) {            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2]=agexact;
     movingaverage(agedeb, fage, ageminpar, mobaverage);            if(nagesqr==1)
   }              cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   if (stepm<=12) stepsize=1;            }
            
   agelim=AGESUP;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   hstepm=1;            savm=oldm;
   hstepm=hstepm/stepm;            oldm=newm;
   yp1=modf(dateintmean,&yp);          } /* end mult */
   anprojmean=yp;        
   yp2=modf((yp1*12),&yp);          s1=s[mw[mi][i]][i];
   mprojmean=yp;          s2=s[mw[mi+1][i]][i];
   yp1=modf((yp2*30.5),&yp);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   jprojmean=yp;          ipmx +=1;
   if(jprojmean==0) jprojmean=1;          sw += weight[i];
   if(mprojmean==0) jprojmean=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
            /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        } /* end of wave */
        } /* end of individual */
   for(cptcov=1;cptcov<=i2;cptcov++){    } /* End of if */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       k=k+1;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       fprintf(ficresf,"\n#******");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for(j=1;j<=cptcoveff;j++) {    return -l;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  }
       }  
       fprintf(ficresf,"******\n");  /*************** log-likelihood *************/
       fprintf(ficresf,"# StartingAge FinalAge");  double funcone( double *x)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  {
          /* Same as likeli but slower because of a lot of printf and if */
          int i, ii, j, k, mi, d, kk;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         fprintf(ficresf,"\n");    double **out;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      double lli; /* Individual log likelihood */
     double llt;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int s1, s2;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double bbh, survp;
           nhstepm = nhstepm/hstepm;    double agexact;
              /*extern weight */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* We are differentiating ll according to initial status */
           oldm=oldms;savm=savms;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*for(i=1;i<imx;i++) 
              printf(" %d\n",s[4][i]);
           for (h=0; h<=nhstepm; h++){    */
             if (h==(int) (calagedate+YEARM*cpt)) {    cov[1]=1.;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  
             }    for(k=1; k<=nlstate; k++) ll[k]=0.;
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               for(i=1; i<=nlstate;i++) {                    for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                 if (mobilav==1)      for(mi=1; mi<= wav[i]-1; mi++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        for (ii=1;ii<=nlstate+ndeath;ii++)
                 else {          for (j=1;j<=nlstate+ndeath;j++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                 }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                          }
               }        for(d=0; d<dh[mi][i]; d++){
               if (h==(int)(calagedate+12*cpt)){          newm=savm;
                 fprintf(ficresf," %.3f", kk1);          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                  cov[2]=agexact;
               }          if(nagesqr==1)
             }            cov[3]= agexact*agexact;
           }          for (kk=1; kk<=cptcovage;kk++) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
         }          }
       }  
     }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                               1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
           /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   fclose(ficresf);          savm=oldm;
 }          oldm=newm;
 /************** Forecasting ******************/        } /* end mult */
 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){        
          s1=s[mw[mi][i]][i];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        s2=s[mw[mi+1][i]][i];
   int *popage;        bbh=(double)bh[mi][i]/(double)stepm; 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        /* bias is positive if real duration
   double *popeffectif,*popcount;         * is higher than the multiple of stepm and negative otherwise.
   double ***p3mat,***tabpop,***tabpopprev;         */
   char filerespop[FILENAMELENGTH];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        } else if  (s2==-2) {
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (j=1,survp=0. ; j<=nlstate; j++) 
   agelim=AGESUP;            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          lli= log(survp);
          }else if (mle==1){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          } else if(mle==2){
            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   strcpy(filerespop,"pop");        } else if(mle==3){  /* exponential inter-extrapolation */
   strcat(filerespop,fileres);          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 */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     printf("Problem with forecast resultfile: %s\n", filerespop);          lli=log(out[s1][s2]); /* Original formula */
   }        } else{  /* mle=0 back to 1 */
   printf("Computing forecasting: result on file '%s' \n", filerespop);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        } /* End of if */
         ipmx +=1;
   if (mobilav==1) {        sw += weight[i];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     movingaverage(agedeb, fage, ageminpar, mobaverage);        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   }        if(globpr){
           fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   stepsize=(int) (stepm+YEARM-1)/YEARM;   %11.6f %11.6f %11.6f ", \
   if (stepm<=12) stepsize=1;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                    2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   agelim=AGESUP;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
              llt +=ll[k]*gipmx/gsw;
   hstepm=1;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   hstepm=hstepm/stepm;          }
            fprintf(ficresilk," %10.6f\n", -llt);
   if (popforecast==1) {        }
     if((ficpop=fopen(popfile,"r"))==NULL) {      } /* end of wave */
       printf("Problem with population file : %s\n",popfile);exit(0);    } /* end of individual */
     }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     popage=ivector(0,AGESUP);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     popeffectif=vector(0,AGESUP);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     popcount=vector(0,AGESUP);    if(globpr==0){ /* First time we count the contributions and weights */
          gipmx=ipmx;
     i=1;        gsw=sw;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    }
        return -l;
     imx=i;  }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }  
   /*************** function likelione ***********/
   for(cptcov=1;cptcov<=i2;cptcov++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  {
       k=k+1;    /* This routine should help understanding what is done with 
       fprintf(ficrespop,"\n#******");       the selection of individuals/waves and
       for(j=1;j<=cptcoveff;j++) {       to check the exact contribution to the likelihood.
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       Plotting could be done.
       }     */
       fprintf(ficrespop,"******\n");    int k;
       fprintf(ficrespop,"# Age");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    if(*globpri !=0){ /* Just counts and sums, no printings */
       if (popforecast==1)  fprintf(ficrespop," [Population]");      strcpy(fileresilk,"ilk"); 
            strcat(fileresilk,fileres);
       for (cpt=0; cpt<=0;cpt++) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          printf("Problem with resultfile: %s\n", fileresilk);
                fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      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");
           nhstepm = nhstepm/hstepm;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
                /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(k=1; k<=nlstate; k++) 
           oldm=oldms;savm=savms;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
            }
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    *fretone=(*funcone)(p);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    if(*globpri !=0){
             }      fclose(ficresilk);
             for(j=1; j<=nlstate+ndeath;j++) {      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
               kk1=0.;kk2=0;      fflush(fichtm); 
               for(i=1; i<=nlstate;i++) {                  } 
                 if (mobilav==1)    return;
                   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];  
                 }  /*********** Maximum Likelihood Estimation ***************/
               }  
               if (h==(int)(calagedate+12*cpt)){  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  {
                   /*fprintf(ficrespop," %.3f", kk1);    int i,j, iter=0;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    double **xi;
               }    double fret;
             }    double fretone; /* Only one call to likelihood */
             for(i=1; i<=nlstate;i++){    /*  char filerespow[FILENAMELENGTH];*/
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){  #ifdef NLOPT
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    int creturn;
                 }    nlopt_opt opt;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    /* 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 */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    double * p1; /* Shifted parameters from 0 instead of 1 */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    myfunc_data dinst, *d = &dinst;
           }  #endif
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }  
       }    xi=matrix(1,npar,1,npar);
      for (i=1;i<=npar;i++)
   /******/      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      strcpy(filerespow,"pow"); 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    strcat(filerespow,fileres);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           nhstepm = nhstepm/hstepm;      printf("Problem with resultfile: %s\n", filerespow);
                fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
           oldm=oldms;savm=savms;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      for (i=1;i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){      for(j=1;j<=nlstate+ndeath;j++)
             if (h==(int) (calagedate+YEARM*cpt)) {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficrespow,"\n");
             }  #ifdef POWELL
             for(j=1; j<=nlstate+ndeath;j++) {    powell(p,xi,npar,ftol,&iter,&fret,func);
               kk1=0.;kk2=0;  #endif
               for(i=1; i<=nlstate;i++) {                
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      #ifdef NLOPT
               }  #ifdef NEWUOA
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
             }  #else
           }    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #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);
      
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     d->function = func;
   if (popforecast==1) {    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     free_ivector(popage,0,AGESUP);    nlopt_set_min_objective(opt, myfunc, d);
     free_vector(popeffectif,0,AGESUP);    nlopt_set_xtol_rel(opt, ftol);
     free_vector(popcount,0,AGESUP);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
   }      printf("nlopt failed! %d\n",creturn); 
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    else {
   fclose(ficrespop);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
 }      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
 /***********************************************/    }
 /**************** Main Program *****************/    nlopt_destroy(opt);
 /***********************************************/  #endif
     free_matrix(xi,1,npar,1,npar);
 int main(int argc, char *argv[])    fclose(ficrespow);
 {    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   double agedeb, agefin,hf;  
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  }
   
   double fret;  /**** Computes Hessian and covariance matrix ***/
   double **xi,tmp,delta;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
   double dum; /* Dummy variable */    double  **a,**y,*x,pd;
   double ***p3mat;    double **hess;
   int *indx;    int i, j;
   char line[MAXLINE], linepar[MAXLINE];    int *indx;
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      void lubksb(double **a, int npar, int *indx, double b[]) ;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
   char filerest[FILENAMELENGTH];    hess=matrix(1,npar,1,npar);
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];    printf("\nCalculation of the hessian matrix. Wait...\n");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   int firstobs=1, lastobs=10;    for (i=1;i<=npar;i++){
   int sdeb, sfin; /* Status at beginning and end */      printf("%d",i);fflush(stdout);
   int c,  h , cpt,l;      fprintf(ficlog,"%d",i);fflush(ficlog);
   int ju,jl, mi;     
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      
   int mobilav=0,popforecast=0;      /*  printf(" %f ",p[i]);
   int hstepm, nhstepm;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    }
     
   double bage, fage, age, agelim, agebase;    for (i=1;i<=npar;i++) {
   double ftolpl=FTOL;      for (j=1;j<=npar;j++)  {
   double **prlim;        if (j>i) { 
   double *severity;          printf(".%d%d",i,j);fflush(stdout);
   double ***param; /* Matrix of parameters */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double  *p;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   double **matcov; /* Matrix of covariance */          
   double ***delti3; /* Scale */          hess[j][i]=hess[i][j];    
   double *delti; /* Scale */          /*printf(" %lf ",hess[i][j]);*/
   double ***eij, ***vareij;        }
   double **varpl; /* Variances of prevalence limits by age */      }
   double *epj, vepp;    }
   double kk1, kk2;    printf("\n");
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    fprintf(ficlog,"\n");
    
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   char version[80]="Imach version 0.8f, May 2002, INED-EUROREVES ";    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   char *alph[]={"a","a","b","c","d","e"}, str[4];    
     a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
   char z[1]="c", occ;    x=vector(1,npar);
 #include <sys/time.h>    indx=ivector(1,npar);
 #include <time.h>    for (i=1;i<=npar;i++)
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
      ludcmp(a,npar,indx,&pd);
   /* long total_usecs;  
   struct timeval start_time, end_time;    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      x[j]=1;
   getcwd(pathcd, size);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   printf("\n%s",version);        matcov[i][j]=x[i];
   if(argc <=1){      }
     printf("\nEnter the parameter file name: ");    }
     scanf("%s",pathtot);  
   }    printf("\n#Hessian matrix#\n");
   else{    fprintf(ficlog,"\n#Hessian matrix#\n");
     strcpy(pathtot,argv[1]);    for (i=1;i<=npar;i++) { 
   }      for (j=1;j<=npar;j++) { 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        printf("%.3e ",hess[i][j]);
   /*cygwin_split_path(pathtot,path,optionfile);        fprintf(ficlog,"%.3e ",hess[i][j]);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      }
   /* cutv(path,optionfile,pathtot,'\\');*/      printf("\n");
       fprintf(ficlog,"\n");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);    /* Recompute Inverse */
   replace(pathc,path);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 /*-------- arguments in the command line --------*/    ludcmp(a,npar,indx,&pd);
   
   strcpy(fileres,"r");    /*  printf("\n#Hessian matrix recomputed#\n");
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   /*---------arguments file --------*/      x[j]=1;
       lubksb(a,npar,indx,x);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      for (i=1;i<=npar;i++){ 
     printf("Problem with optionfile %s\n",optionfile);        y[i][j]=x[i];
     goto end;        printf("%.3e ",y[i][j]);
   }        fprintf(ficlog,"%.3e ",y[i][j]);
       }
   strcpy(filereso,"o");      printf("\n");
   strcat(filereso,fileres);      fprintf(ficlog,"\n");
   if((ficparo=fopen(filereso,"w"))==NULL) {    }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    */
   }  
     free_matrix(a,1,npar,1,npar);
   /* Reads comments: lines beginning with '#' */    free_matrix(y,1,npar,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_vector(x,1,npar);
     ungetc(c,ficpar);    free_ivector(indx,1,npar);
     fgets(line, MAXLINE, ficpar);    free_matrix(hess,1,npar,1,npar);
     puts(line);  
     fputs(line,ficparo);  
   }  }
   ungetc(c,ficpar);  
   /*************** hessian matrix ****************/
   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);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   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);    int i;
 while((c=getc(ficpar))=='#' && c!= EOF){    int l=1, lmax=20;
     ungetc(c,ficpar);    double k1,k2;
     fgets(line, MAXLINE, ficpar);    double p2[MAXPARM+1]; /* identical to x */
     puts(line);    double res;
     fputs(line,ficparo);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   }    double fx;
   ungetc(c,ficpar);    int k=0,kmax=10;
      double l1;
      
   covar=matrix(0,NCOVMAX,1,n);    fx=func(x);
   cptcovn=0;    for (i=1;i<=npar;i++) p2[i]=x[i];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       l1=pow(10,l);
   ncovmodel=2+cptcovn;      delts=delt;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      for(k=1 ; k <kmax; k=k+1){
          delt = delta*(l1*k);
   /* Read guess parameters */        p2[theta]=x[theta] +delt;
   /* Reads comments: lines beginning with '#' */        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   while((c=getc(ficpar))=='#' && c!= EOF){        p2[theta]=x[theta]-delt;
     ungetc(c,ficpar);        k2=func(p2)-fx;
     fgets(line, MAXLINE, ficpar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     puts(line);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     fputs(line,ficparo);        
   }  #ifdef DEBUGHESS
   ungetc(c,ficpar);        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);
          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);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  #endif
     for(i=1; i <=nlstate; i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     for(j=1; j <=nlstate+ndeath-1; j++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       fscanf(ficpar,"%1d%1d",&i1,&j1);          k=kmax;
       fprintf(ficparo,"%1d%1d",i1,j1);        }
       printf("%1d%1d",i,j);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for(k=1; k<=ncovmodel;k++){          k=kmax; l=lmax*10;
         fscanf(ficpar," %lf",&param[i][j][k]);        }
         printf(" %lf",param[i][j][k]);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         fprintf(ficparo," %lf",param[i][j][k]);          delts=delt;
       }        }
       fscanf(ficpar,"\n");      }
       printf("\n");    }
       fprintf(ficparo,"\n");    delti[theta]=delts;
     }    return res; 
      
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  }
   
   p=param[1][1];  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
    {
   /* Reads comments: lines beginning with '#' */    int i;
   while((c=getc(ficpar))=='#' && c!= EOF){    int l=1, lmax=20;
     ungetc(c,ficpar);    double k1,k2,k3,k4,res,fx;
     fgets(line, MAXLINE, ficpar);    double p2[MAXPARM+1];
     puts(line);    int k;
     fputs(line,ficparo);  
   }    fx=func(x);
   ungetc(c,ficpar);    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      p2[thetai]=x[thetai]+delti[thetai]/k;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   for(i=1; i <=nlstate; i++){      k1=func(p2)-fx;
     for(j=1; j <=nlstate+ndeath-1; j++){    
       fscanf(ficpar,"%1d%1d",&i1,&j1);      p2[thetai]=x[thetai]+delti[thetai]/k;
       printf("%1d%1d",i,j);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       fprintf(ficparo,"%1d%1d",i1,j1);      k2=func(p2)-fx;
       for(k=1; k<=ncovmodel;k++){    
         fscanf(ficpar,"%le",&delti3[i][j][k]);      p2[thetai]=x[thetai]-delti[thetai]/k;
         printf(" %le",delti3[i][j][k]);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         fprintf(ficparo," %le",delti3[i][j][k]);      k3=func(p2)-fx;
       }    
       fscanf(ficpar,"\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
       printf("\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       fprintf(ficparo,"\n");      k4=func(p2)-fx;
     }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   }  #ifdef DEBUG
   delti=delti3[1][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);
   /* Reads comments: lines beginning with '#' */  #endif
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    return res;
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /************** Inverse of matrix **************/
   }  void ludcmp(double **a, int n, int *indx, double *d) 
   ungetc(c,ficpar);  { 
      int i,imax,j,k; 
   matcov=matrix(1,npar,1,npar);    double big,dum,sum,temp; 
   for(i=1; i <=npar; i++){    double *vv; 
     fscanf(ficpar,"%s",&str);   
     printf("%s",str);    vv=vector(1,n); 
     fprintf(ficparo,"%s",str);    *d=1.0; 
     for(j=1; j <=i; j++){    for (i=1;i<=n;i++) { 
       fscanf(ficpar," %le",&matcov[i][j]);      big=0.0; 
       printf(" %.5le",matcov[i][j]);      for (j=1;j<=n;j++) 
       fprintf(ficparo," %.5le",matcov[i][j]);        if ((temp=fabs(a[i][j])) > big) big=temp; 
     }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     fscanf(ficpar,"\n");      vv[i]=1.0/big; 
     printf("\n");    } 
     fprintf(ficparo,"\n");    for (j=1;j<=n;j++) { 
   }      for (i=1;i<j;i++) { 
   for(i=1; i <=npar; i++)        sum=a[i][j]; 
     for(j=i+1;j<=npar;j++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       matcov[i][j]=matcov[j][i];        a[i][j]=sum; 
          } 
   printf("\n");      big=0.0; 
       for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
     /*-------- Rewriting paramater file ----------*/        for (k=1;k<j;k++) 
      strcpy(rfileres,"r");    /* "Rparameterfile */          sum -= a[i][k]*a[k][j]; 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        a[i][j]=sum; 
      strcat(rfileres,".");    /* */        if ( (dum=vv[i]*fabs(sum)) >= big) { 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          big=dum; 
     if((ficres =fopen(rfileres,"w"))==NULL) {          imax=i; 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        } 
     }      } 
     fprintf(ficres,"#%s\n",version);      if (j != imax) { 
            for (k=1;k<=n;k++) { 
     /*-------- data file ----------*/          dum=a[imax][k]; 
     if((fic=fopen(datafile,"r"))==NULL)    {          a[imax][k]=a[j][k]; 
       printf("Problem with datafile: %s\n", datafile);goto end;          a[j][k]=dum; 
     }        } 
         *d = -(*d); 
     n= lastobs;        vv[imax]=vv[j]; 
     severity = vector(1,maxwav);      } 
     outcome=imatrix(1,maxwav+1,1,n);      indx[j]=imax; 
     num=ivector(1,n);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     moisnais=vector(1,n);      if (j != n) { 
     annais=vector(1,n);        dum=1.0/(a[j][j]); 
     moisdc=vector(1,n);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     andc=vector(1,n);      } 
     agedc=vector(1,n);    } 
     cod=ivector(1,n);    free_vector(vv,1,n);  /* Doesn't work */
     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);  void lubksb(double **a, int n, int *indx, double b[]) 
     s=imatrix(1,maxwav+1,1,n);  { 
     adl=imatrix(1,maxwav+1,1,n);        int i,ii=0,ip,j; 
     tab=ivector(1,NCOVMAX);    double sum; 
     ncodemax=ivector(1,8);   
     for (i=1;i<=n;i++) { 
     i=1;      ip=indx[i]; 
     while (fgets(line, MAXLINE, fic) != NULL)    {      sum=b[ip]; 
       if ((i >= firstobs) && (i <=lastobs)) {      b[ip]=b[i]; 
              if (ii) 
         for (j=maxwav;j>=1;j--){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      else if (sum) ii=i; 
           strcpy(line,stra);      b[i]=sum; 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    } 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for (i=n;i>=1;i--) { 
         }      sum=b[i]; 
              for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      b[i]=sum/a[i][i]; 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    } 
   } 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  void pstamp(FILE *fichier)
   {
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
         for (j=ncovcol;j>=1;j--){  }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  /************ Frequencies ********************/
         num[i]=atol(stra);  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 */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    int i, m, jk, j1, bool, z1,j;
     int first;
         i=i+1;    double ***freq; /* Frequencies */
       }    double *pp, **prop;
     }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     /* printf("ii=%d", ij);    char fileresp[FILENAMELENGTH];
        scanf("%d",i);*/    
   imx=i-1; /* Number of individuals */    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
   /* for (i=1; i<=imx; i++){    strcpy(fileresp,"p");
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    strcat(fileresp,fileres);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    if((ficresp=fopen(fileresp,"w"))==NULL) {
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      printf("Problem with prevalence resultfile: %s\n", fileresp);
     }*/      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
    /*  for (i=1; i<=imx; i++){      exit(0);
      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]));}*/    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
      j1=0;
      
   /* Calculation of the number of parameter from char model*/    j=cptcoveff;
   Tvar=ivector(1,15);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);    first=1;
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);          /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
        /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   if (strlen(model) >1){    /*    j1++; */
     j=0, j1=0, k1=1, k2=1;    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
     j=nbocc(model,'+');        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     j1=nbocc(model,'*');          scanf("%d", i);*/
     cptcovn=j+1;        for (i=-5; i<=nlstate+ndeath; i++)  
     cptcovprod=j1;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
                for(m=iagemin; m <= iagemax+3; m++)
     strcpy(modelsav,model);              freq[i][jk][m]=0;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        
       printf("Error. Non available option model=%s ",model);        for (i=1; i<=nlstate; i++)  
       goto end;          for(m=iagemin; m <= iagemax+3; m++)
     }            prop[i][m]=0;
            
     for(i=(j+1); i>=1;i--){        dateintsum=0;
       cutv(stra,strb,modelsav,'+');        k2cpt=0;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        for (i=1; i<=imx; i++) {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          bool=1;
       /*scanf("%d",i);*/          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
       if (strchr(strb,'*')) {            for (z1=1; z1<=cptcoveff; z1++)       
         cutv(strd,strc,strb,'*');              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
         if (strcmp(strc,"age")==0) {                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
           cptcovprod--;                bool=0;
           cutv(strb,stre,strd,'V');                /* 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", 
           Tvar[i]=atoi(stre);                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
           cptcovage++;                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
             Tage[cptcovage]=i;                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
             /*printf("stre=%s ", stre);*/              } 
         }          }
         else if (strcmp(strd,"age")==0) {   
           cptcovprod--;          if (bool==1){
           cutv(strb,stre,strc,'V');            for(m=firstpass; m<=lastpass; m++){
           Tvar[i]=atoi(stre);              k2=anint[m][i]+(mint[m][i]/12.);
           cptcovage++;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
           Tage[cptcovage]=i;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         else {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
           cutv(strb,stre,strc,'V');                if (m<lastpass) {
           Tvar[i]=ncovcol+k1;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           cutv(strb,strc,strd,'V');                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           Tprod[k1]=i;                }
           Tvard[k1][1]=atoi(strc);                
           Tvard[k1][2]=atoi(stre);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           Tvar[cptcovn+k2]=Tvard[k1][1];                  dateintsum=dateintsum+k2;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                  k2cpt++;
           for (k=1; k<=lastobs;k++)                }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                /*}*/
           k1++;            }
           k2=k2+2;          }
         }        } /* end i */
       }         
       else {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        pstamp(ficresp);
        /*  scanf("%d",i);*/        if  (cptcovn>0) {
       cutv(strd,strc,strb,'V');          fprintf(ficresp, "\n#********** Variable "); 
       Tvar[i]=atoi(strc);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresp, "**********\n#");
       strcpy(modelsav,stra);            fprintf(ficlog, "\n#********** Variable "); 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         scanf("%d",i);*/          fprintf(ficlog, "**********\n#");
     }        }
 }        for(i=1; i<=nlstate;i++) 
            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        fprintf(ficresp, "\n");
   printf("cptcovprod=%d ", cptcovprod);        
   scanf("%d ",i);*/        for(i=iagemin; i <= iagemax+3; i++){
     fclose(fic);          if(i==iagemax+3){
             fprintf(ficlog,"Total");
     /*  if(mle==1){*/          }else{
     if (weightopt != 1) { /* Maximisation without weights*/            if(first==1){
       for(i=1;i<=n;i++) weight[i]=1.0;              first=0;
     }              printf("See log file for details...\n");
     /*-calculation of age at interview from date of interview and age at death -*/            }
     agev=matrix(1,maxwav,1,imx);            fprintf(ficlog,"Age %d", i);
           }
     for (i=1; i<=imx; i++) {          for(jk=1; jk <=nlstate ; jk++){
       for(m=2; (m<= maxwav); m++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){              pp[jk] += freq[jk][m][i]; 
          anint[m][i]=9999;          }
          s[m][i]=-1;          for(jk=1; jk <=nlstate ; jk++){
        }            for(m=-1, pos=0; m <=0 ; m++)
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;              pos += freq[jk][m][i];
       }            if(pp[jk]>=1.e-10){
     }              if(first==1){
                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for (i=1; i<=imx; i++)  {              }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for(m=1; (m<= maxwav); m++){            }else{
         if(s[m][i] >0){              if(first==1)
           if (s[m][i] >= nlstate+1) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             if(agedc[i]>0)              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               if(moisdc[i]!=99 && andc[i]!=9999)            }
                 agev[m][i]=agedc[i];          }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {          for(jk=1; jk <=nlstate ; jk++){
               if (andc[i]!=9999){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              pp[jk] += freq[jk][m][i];
               agev[m][i]=-1;          }       
               }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             }            pos += pp[jk];
           }            posprop += prop[jk][i];
           else if(s[m][i] !=9){ /* Should no more exist */          }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for(jk=1; jk <=nlstate ; jk++){
             if(mint[m][i]==99 || anint[m][i]==9999)            if(pos>=1.e-5){
               agev[m][i]=1;              if(first==1)
             else if(agev[m][i] <agemin){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               agemin=agev[m][i];              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/            }else{
             }              if(first==1)
             else if(agev[m][i] >agemax){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               agemax=agev[m][i];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            }
             }            if( i <= iagemax){
             /*agev[m][i]=anint[m][i]-annais[i];*/              if(pos>=1.e-5){
             /*   agev[m][i] = age[i]+2*m;*/                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           }                /*probs[i][jk][j1]= pp[jk]/pos;*/
           else { /* =9 */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
             agev[m][i]=1;              }
             s[m][i]=-1;              else
           }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         }            }
         else /*= 0 Unknown */          }
           agev[m][i]=1;          
       }          for(jk=-1; jk <=nlstate+ndeath; jk++)
                for(m=-1; m <=nlstate+ndeath; m++)
     }              if(freq[jk][m][i] !=0 ) {
     for (i=1; i<=imx; i++)  {              if(first==1)
       for(m=1; (m<= maxwav); m++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         if (s[m][i] > (nlstate+ndeath)) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           printf("Error: Wrong value in nlstate or ndeath\n");                }
           goto end;          if(i <= iagemax)
         }            fprintf(ficresp,"\n");
       }          if(first==1)
     }            printf("Others in log...\n");
           fprintf(ficlog,"\n");
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        }
         /*}*/
     free_vector(severity,1,maxwav);    }
     free_imatrix(outcome,1,maxwav+1,1,n);    dateintmean=dateintsum/k2cpt; 
     free_vector(moisnais,1,n);   
     free_vector(annais,1,n);    fclose(ficresp);
     /* free_matrix(mint,1,maxwav,1,n);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
        free_matrix(anint,1,maxwav,1,n);*/    free_vector(pp,1,nlstate);
     free_vector(moisdc,1,n);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     free_vector(andc,1,n);    /* End of Freq */
   }
      
     wav=ivector(1,imx);  /************ Prevalence ********************/
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  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)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  {  
        /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     /* Concatenates waves */       in each health status at the date of interview (if between dateprev1 and dateprev2).
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       We still use firstpass and lastpass as another selection.
     */
    
       Tcode=ivector(1,100);    int i, m, jk, j1, bool, z1,j;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;    double **prop;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    double posprop; 
          double  y2; /* in fractional years */
    codtab=imatrix(1,100,1,10);    int iagemin, iagemax;
    h=0;    int first; /** to stop verbosity which is redirected to log file */
    m=pow(2,cptcoveff);  
      iagemin= (int) agemin;
    for(k=1;k<=cptcoveff; k++){    iagemax= (int) agemax;
      for(i=1; i <=(m/pow(2,k));i++){    /*pp=vector(1,nlstate);*/
        for(j=1; j <= ncodemax[k]; j++){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
            h++;    j1=0;
            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]);*/    /*j=cptcoveff;*/
          }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
        }    
      }    first=1;
    }    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      /*for(i1=1; i1<=ncodemax[k1];i1++){
       codtab[1][2]=1;codtab[2][2]=2; */        j1++;*/
    /* for(i=1; i <=m ;i++){        
       for(k=1; k <=cptcovn; k++){        for (i=1; i<=nlstate; i++)  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          for(m=iagemin; m <= iagemax+3; m++)
       }            prop[i][m]=0.0;
       printf("\n");       
       }        for (i=1; i<=imx; i++) { /* Each individual */
       scanf("%d",i);*/          bool=1;
              if  (cptcovn>0) {
    /* Calculates basic frequencies. Computes observed prevalence at single age            for (z1=1; z1<=cptcoveff; z1++) 
        and prints on file fileres'p'. */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
              } 
              if (bool==1) { 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                      if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     /* For Powell, parameters are in a vector p[] starting at p[1]                if (s[m][i]>0 && s[m][i]<=nlstate) { 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
     if(mle==1){                } 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              }
     }            } /* end selection of waves */
              }
     /*--------- 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);        for(i=iagemin; i <= iagemax+3; i++){  
            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
    jk=1;          } 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          for(jk=1; jk <=nlstate ; jk++){     
    for(i=1,jk=1; i <=nlstate; i++){            if( i <=  iagemax){ 
      for(k=1; k <=(nlstate+ndeath); k++){              if(posprop>=1.e-5){ 
        if (k != i)                probs[i][jk][j1]= prop[jk][i]/posprop;
          {              } else{
            printf("%d%d ",i,k);                if(first==1){
            fprintf(ficres,"%1d%1d ",i,k);                  first=0;
            for(j=1; j <=ncovmodel; j++){                  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]);
              printf("%f ",p[jk]);                }
              fprintf(ficres,"%f ",p[jk]);              }
              jk++;            } 
            }          }/* end jk */ 
            printf("\n");        }/* end i */ 
            fprintf(ficres,"\n");      /*} *//* end i1 */
          }    } /* end j1 */
      }    
    }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
  if(mle==1){    /*free_vector(pp,1,nlstate);*/
     /* Computing hessian and covariance matrix */    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     ftolhess=ftol; /* Usually correct */  }  /* End of prevalence */
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }  /************* Waves Concatenation ***************/
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
     printf("# Scales (for hessian or gradient estimation)\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)
      for(i=1,jk=1; i <=nlstate; i++){  {
       for(j=1; j <=nlstate+ndeath; j++){    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         if (j!=i) {       Death is a valid wave (if date is known).
           fprintf(ficres,"%1d%1d",i,j);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           printf("%1d%1d",i,j);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           for(k=1; k<=ncovmodel;k++){       and mw[mi+1][i]. dh depends on stepm.
             printf(" %.5e",delti[jk]);       */
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;    int i, mi, m;
           }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           printf("\n");       double sum=0., jmean=0.;*/
           fprintf(ficres,"\n");    int first;
         }    int j, k=0,jk, ju, jl;
       }    double sum=0.;
      }    first=0;
        jmin=100000;
     k=1;    jmax=-1;
     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");    jmean=0.;
     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<=imx; i++){
     for(i=1;i<=npar;i++){      mi=0;
       /*  if (k>nlstate) k=1;      m=firstpass;
       i1=(i-1)/(ncovmodel*nlstate)+1;      while(s[m][i] <= nlstate){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       printf("%s%d%d",alph[k],i1,tab[i]);*/          mw[++mi][i]=m;
       fprintf(ficres,"%3d",i);        if(m >=lastpass)
       printf("%3d",i);          break;
       for(j=1; j<=i;j++){        else
         fprintf(ficres," %.5e",matcov[i][j]);          m++;
         printf(" %.5e",matcov[i][j]);      }/* end while */
       }      if (s[m][i] > nlstate){
       fprintf(ficres,"\n");        mi++;     /* Death is another wave */
       printf("\n");        /* if(mi==0)  never been interviewed correctly before death */
       k++;           /* Only death is a correct wave */
     }        mw[mi][i]=m;
          }
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);      wav[i]=mi;
       fgets(line, MAXLINE, ficpar);      if(mi==0){
       puts(line);        nbwarn++;
       fputs(line,ficparo);        if(first==0){
     }          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     ungetc(c,ficpar);          first=1;
     estepm=0;        }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        if(first==1){
     if (estepm==0 || estepm < stepm) estepm=stepm;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     if (fage <= 2) {        }
       bage = ageminpar;      } /* end mi==0 */
       fage = agemaxpar;    } /* End individuals */
     }  
        for(i=1; i<=imx; i++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      for(mi=1; mi<wav[i];mi++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        if (stepm <=0)
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          dh[mi][i]=1;
          else{
     while((c=getc(ficpar))=='#' && c!= EOF){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     ungetc(c,ficpar);            if (agedc[i] < 2*AGESUP) {
     fgets(line, MAXLINE, ficpar);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     puts(line);              if(j==0) j=1;  /* Survives at least one month after exam */
     fputs(line,ficparo);              else if(j<0){
   }                nberr++;
   ungetc(c,ficpar);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  j=1; /* Temporary Dangerous patch */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                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(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                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);
                    }
   while((c=getc(ficpar))=='#' && c!= EOF){              k=k+1;
     ungetc(c,ficpar);              if (j >= jmax){
     fgets(line, MAXLINE, ficpar);                jmax=j;
     puts(line);                ijmax=i;
     fputs(line,ficparo);              }
   }              if (j <= jmin){
   ungetc(c,ficpar);                jmin=j;
                  ijmin=i;
               }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;              sum=sum+j;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              /*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);*/
   fscanf(ficpar,"pop_based=%d\n",&popbased);            }
   fprintf(ficparo,"pop_based=%d\n",popbased);            }
   fprintf(ficres,"pop_based=%d\n",popbased);            else{
              j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   while((c=getc(ficpar))=='#' && c!= EOF){  /*        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]); */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);            k=k+1;
     puts(line);            if (j >= jmax) {
     fputs(line,ficparo);              jmax=j;
   }              ijmax=i;
   ungetc(c,ficpar);            }
             else if (j <= jmin){
   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);              jmin=j;
 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);              ijmin=i;
 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);            }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
 while((c=getc(ficpar))=='#' && c!= EOF){            if(j<0){
     ungetc(c,ficpar);              nberr++;
     fgets(line, MAXLINE, ficpar);              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]);
     puts(line);              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]);
     fputs(line,ficparo);            }
   }            sum=sum+j;
   ungetc(c,ficpar);          }
           jk= j/stepm;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          jl= j -jk*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);          ju= j -(jk+1)*stepm;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              dh[mi][i]=jk;
               bh[mi][i]=0;
 /*------------ gnuplot -------------*/            }else{ /* We want a negative bias in order to only have interpolation ie
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);                    * to avoid the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
 /*------------ free_vector  -------------*/              bh[mi][i]=ju;
  chdir(path);            }
            }else{
  free_ivector(wav,1,imx);            if(jl <= -ju){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              dh[mi][i]=jk;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                bh[mi][i]=jl;       /* bias is positive if real duration
  free_ivector(num,1,n);                                   * is higher than the multiple of stepm and negative otherwise.
  free_vector(agedc,1,n);                                   */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            }
  fclose(ficparo);            else{
  fclose(ficres);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
 /*--------- index.htm --------*/            }
             if(dh[mi][i]==0){
  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);              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
                /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   /*--------------- Prevalence limit --------------*/            }
            } /* end if mle */
   strcpy(filerespl,"pl");        }
   strcat(filerespl,fileres);      } /* end wave */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    jmean=sum/k;
   }    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("Computing prevalence limit: result on file '%s' \n", filerespl);    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);
   fprintf(ficrespl,"#Prevalence limit\n");   }
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  /*********** Tricode ****************************/
   fprintf(ficrespl,"\n");  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
    {
   prlim=matrix(1,nlstate,1,nlstate);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     * Boring subroutine which should only output nbcode[Tvar[j]][k]
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     * nbcode[Tvar[j]][1]= 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    */
   k=0;  
   agebase=ageminpar;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   agelim=agemaxpar;    int modmaxcovj=0; /* Modality max of covariates j */
   ftolpl=1.e-10;    int cptcode=0; /* Modality max of covariates j */
   i1=cptcoveff;    int modmincovj=0; /* Modality min of covariates j */
   if (cptcovn < 1){i1=1;}  
   
   for(cptcov=1;cptcov<=i1;cptcov++){    cptcoveff=0; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   
         k=k+1;    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");    /* Loop on covariates without age and products */
         for(j=1;j<=cptcoveff;j++)    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for (k=-1; k < maxncov; k++) Ndum[k]=0;
         fprintf(ficrespl,"******\n");      for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
                                         modality of this covariate Vj*/ 
         for (age=agebase; age<=agelim; age++){        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                                      * If product of Vn*Vm, still boolean *:
           fprintf(ficrespl,"%.0f",age );                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
           for(i=1; i<=nlstate;i++)                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
           fprintf(ficrespl," %.5f", prlim[i][i]);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
           fprintf(ficrespl,"\n");                                        modality of the nth covariate of individual i. */
         }        if (ij > modmaxcovj)
       }          modmaxcovj=ij; 
     }        else if (ij < modmincovj) 
   fclose(ficrespl);          modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
   /*------------- h Pij x at various ages ------------*/          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
            exit(1);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        }else
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   printf("Computing pij: result on file '%s' \n", filerespij);        /* 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
   stepsize=(int) (stepm+YEARM-1)/YEARM;           female is 1, then modmaxcovj=1.*/
   /*if (stepm<=24) stepsize=2;*/      } /* end for loop on individuals i */
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   agelim=AGESUP;      fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   hstepm=stepsize*YEARM; /* Every year of age */      cptcode=modmaxcovj;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       /*for (i=0; i<=cptcode; i++) {*/
   k=0;      for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
   for(cptcov=1;cptcov<=i1;cptcov++){        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
       k=k+1;        if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
         fprintf(ficrespij,"\n#****** ");          if( k != -1){
         for(j=1;j<=cptcoveff;j++)            ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                               covariate for which somebody answered excluding 
         fprintf(ficrespij,"******\n");                               undefined. Usually 2: 0 and 1. */
                  }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                               covariate for which somebody answered including 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                               undefined. Usually 3: -1, 0 and 1. */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           oldm=oldms;savm=savms;        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);             historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           fprintf(ficrespij,"# Age");      } /* Ndum[-1] number of undefined modalities */
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
               fprintf(ficrespij," %1d-%1d",i,j);      /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
           fprintf(ficrespij,"\n");         If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
            for (h=0; h<=nhstepm; h++){         modmincovj=3; modmaxcovj = 7;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );         There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
             for(i=1; i<=nlstate;i++)         which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
               for(j=1; j<=nlstate+ndeath;j++)         defining two dummy variables: variables V1_1 and V1_2.
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);         nbcode[Tvar[j]][ij]=k;
             fprintf(ficrespij,"\n");         nbcode[Tvar[j]][1]=0;
              }         nbcode[Tvar[j]][2]=1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         nbcode[Tvar[j]][3]=2;
           fprintf(ficrespij,"\n");      */
         }      ij=0; /* ij is similar to i but can jumps over null modalities */
     }      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/
   }          if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */
             break;
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          }
           ij++;
   fclose(ficrespij);          nbcode[Tvar[j]][ij]=i;  /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
           cptcode = ij; /* New max modality for covar j */
       } /* end of loop on modality i=-1 to 1 or more */
   /*---------- Forecasting ------------------*/        
   if((stepm == 1) && (strcmp(model,".")==0)){      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      /*  /\*recode from 0 *\/ */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      /*                               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; */
   else{      /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
     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);      /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
   }      /*  if (ij > ncodemax[j]) { */
        /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
       /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
   /*---------- Health expectancies and variances ------------*/      /*    break; */
       /*  } */
   strcpy(filerest,"t");      /*   }  /\* end of loop on modality k *\/ */
   strcat(filerest,fileres);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   if((ficrest=fopen(filerest,"w"))==NULL) {    
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   }    
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
      /* 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 */ 
   strcpy(filerese,"e");     Ndum[ij]++; /* Might be supersed V1 + V1*age */
   strcat(filerese,fileres);   } 
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);   ij=0;
   }   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      if((Ndum[i]!=0) && (i<=ncovcol)){
  strcpy(fileresv,"v");       ij++;
   strcat(fileresv,fileres);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       Tvaraff[ij]=i; /*For printing (unclear) */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);     }else{
   }         /* Tvaraff[ij]=0; */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     }
   calagedate=-1;   }
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   /* ij--; */
    cptcoveff=ij; /*Number of total covariates*/
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){  }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  
       fprintf(ficrest,"\n#****** ");  /*********** Health Expectancies ****************/
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
       fprintf(ficrest,"******\n");  
   {
       fprintf(ficreseij,"\n#****** ");    /* Health expectancies, no variances */
       for(j=1;j<=cptcoveff;j++)    int i, j, nhstepm, hstepm, h, nstepm;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int nhstepma, nstepma; /* Decreasing with age */
       fprintf(ficreseij,"******\n");    double age, agelim, hf;
     double ***p3mat;
       fprintf(ficresvij,"\n#****** ");    double eip;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    pstamp(ficreseij);
       fprintf(ficresvij,"******\n");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for(i=1; i<=nlstate;i++){
       oldm=oldms;savm=savms;      for(j=1; j<=nlstate;j++){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);          fprintf(ficreseij," e%1d%1d ",i,j);
        }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      fprintf(ficreseij," e%1d. ",i);
       oldm=oldms;savm=savms;    }
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    fprintf(ficreseij,"\n");
      
     
      if(estepm < stepm){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      printf ("Problem %d lower than %d\n",estepm, stepm);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    }
       fprintf(ficrest,"\n");    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
       epj=vector(1,nlstate+1);     * This is mainly to measure the difference between two models: for example
       for(age=bage; age <=fage ;age++){     * if stepm=24 months pijx are given only every 2 years and by summing them
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     * we are calculating an estimate of the Life Expectancy assuming a linear 
         if (popbased==1) {     * progression in between and thus overestimating or underestimating according
           for(i=1; i<=nlstate;i++)     * to the curvature of the survival function. If, for the same date, we 
             prlim[i][i]=probs[(int)age][i][k];     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         }     * to compare the new estimate of Life expectancy with the same linear 
             * hypothesis. A more precise result, taking into account a more precise
         fprintf(ficrest," %4.0f",age);     * curvature will be obtained if estepm is as small as stepm. */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    /* For example we decided to compute the life expectancy with the smallest unit */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/       nhstepm is the number of hstepm from age to agelim 
           }       nstepm is the number of stepm from age to agelin. 
           epj[nlstate+1] +=epj[j];       Look at hpijx to understand the reason of that which relies in memory size
         }       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         for(i=1, vepp=0.;i <=nlstate;i++)       survival function given by stepm (the optimization length). Unfortunately it
           for(j=1;j <=nlstate;j++)       means that if the survival funtion is printed only each two years of age and if
             vepp += vareij[i][j][(int)age];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));       results. So we changed our mind and took the option of the best precision.
         for(j=1;j <=nlstate;j++){    */
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         }  
         fprintf(ficrest,"\n");    agelim=AGESUP;
       }    /* If stepm=6 months */
     }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 free_matrix(mint,1,maxwav,1,n);      
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  /* nhstepm age range expressed in number of stepm */
     free_vector(weight,1,n);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   fclose(ficreseij);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fclose(ficresvij);    /* if (stepm >= YEARM) hstepm=1;*/
   fclose(ficrest);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   fclose(ficpar);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_vector(epj,1,nlstate+1);  
      for (age=bage; age<=fage; age ++){ 
   /*------- Variance limit prevalence------*/        nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   strcpy(fileresvpl,"vpl");      /* if (stepm >= YEARM) hstepm=1;*/
   strcat(fileresvpl,fileres);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      /* If stepm=6 months */
     exit(0);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   k=0;      
   for(cptcov=1;cptcov<=i1;cptcov++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      
       k=k+1;      printf("%d|",(int)age);fflush(stdout);
       fprintf(ficresvpl,"\n#****** ");      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       for(j=1;j<=cptcoveff;j++)      
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /* Computing expectancies */
       fprintf(ficresvpl,"******\n");      for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++)
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       oldm=oldms;savm=savms;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            
     }            /* 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]);*/
  }  
           }
   fclose(ficresvpl);  
       fprintf(ficreseij,"%3.0f",age );
   /*---------- End : free ----------------*/      for(i=1; i<=nlstate;i++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        eip=0;
          for(j=1; j<=nlstate;j++){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          eip +=eij[i][j][(int)age];
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
          }
          fprintf(ficreseij,"%9.4f", eip );
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      }
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficreseij,"\n");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(matcov,1,npar,1,npar);    printf("\n");
   free_vector(delti,1,npar);    fprintf(ficlog,"\n");
   free_matrix(agev,1,maxwav,1,imx);    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  }
   
   if(erreur >0)  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[] )
     printf("End of Imach with error or warning %d\n",erreur);  
   else   printf("End of Imach\n");  {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /* Covariances of health expectancies eij and of total life expectancies according
       to initial status i, ei. .
   /* 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);*/    */
   /*printf("Total time was %d uSec.\n", total_usecs);*/    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   /*------ End -----------*/    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
  end:    double **dnewm,**doldm;
 #ifdef windows    double *xp, *xm;
   /* chdir(pathcd);*/    double **gp, **gm;
 #endif    double ***gradg, ***trgradg;
  /*system("wgnuplot graph.plt");*/    int theta;
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/    double eip, vip;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
  strcat(plotcmd," ");    xp=vector(1,npar);
  strcat(plotcmd,optionfilegnuplot);    xm=vector(1,npar);
  system(plotcmd);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
 #ifdef windows    
   while (z[0] != 'q') {    pstamp(ficresstdeij);
     /* chdir(path); */    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    fprintf(ficresstdeij,"# Age");
     scanf("%s",z);    for(i=1; i<=nlstate;i++){
     if (z[0] == 'c') system("./imach");      for(j=1; j<=nlstate;j++)
     else if (z[0] == 'e') system(optionfilehtm);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     else if (z[0] == 'g') system(plotcmd);      fprintf(ficresstdeij," e%1d. ",i);
     else if (z[0] == 'q') exit(0);    }
   }    fprintf(ficresstdeij,"\n");
 #endif  
 }    pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           if(nagesqr==1)
             cov[3]= age*age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+nagesqr+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<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+nagesqr+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]]);
            printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
          }
          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> \
    - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Standard deviation 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 */
     fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
     for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficgp,"# initial state %d\n",i);
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           fprintf(ficgp,"#   current state %d\n",k);
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
             jk++; 
           }
           fprintf(ficgp,"\n");
         }
       }
      }
     fprintf(ficgp,"##############\n#\n");
   
     /*goto avoid;*/
     fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
     fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
     fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
     fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
     fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
     fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
     fprintf(ficgp,"#\n");
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        fprintf(ficgp,"# ng=%d\n",ng);
        fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"#    jk=%d\n",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)
                  if(nagesqr==0)
                    fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                else
                  if(nagesqr==0)
                    fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel-nagesqr; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){ 
                  if(nagesqr==0)
                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
     
                  ij=1;
                  for(j=3; j <=ncovmodel-nagesqr; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,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+age*age
      * - nagesqr = 1 if age*age in the model, otherwise 0.
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
      * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
      * - 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];
     char *strpt;
   
     /*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;
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%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;
       }
       strcpy(modelsav,model); 
       if ((strpt=strstr(model,"age*age")) !=0){
         printf(" strpt=%s, model=%s\n",strpt, model);
         if(strpt != model){
         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
    corresponding column of parameters.\n",model);
         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
    corresponding column of parameters.\n",model); fflush(ficlog);
         return 1;
       }
   
         nagesqr=1;
         if (strstr(model,"+age*age") !=0)
           substrchaine(modelsav, model, "+age*age");
         else if (strstr(model,"age*age+") !=0)
           substrchaine(modelsav, model, "age*age+");
         else 
           substrchaine(modelsav, model, "age*age");
       }else
         nagesqr=0;
       if (strlen(modelsav) >1){
         j=nbocc(modelsav,'+'); /**< j=Number of '+' */
         j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
         cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
         cptcovt= j+1; /* Number of total covariates in the model, not including
                      * cst, age and age*age 
                      * V1+V1*age+ V3 + V3*V4+age*age=> 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  */
   
       
         /*   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]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[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; V1+V1*age Tvar[2]=1 */
               cptcovage++; /* Sums the number of covariates which include age as a product */
               Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
               /*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 + on total covariates */
       } /* end if strlen(modelsave == 0) age*age might exist */
     } /* end if strlen(model == 0) */
     
     /*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(int logged)
    {
      /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
   #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-");
              if(logged) fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for "); if (logged) 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) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");if(logged) fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");if(logged) 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"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); if(logged) 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__);
      if(logged) 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);
            if(logged) 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()); 
      if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              if (logged) fprintf(ficlog, "\nThe 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 */
           return 0;
   }
   
   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");
         }
         /*}*/
       }
           return 0;
   }
   
   
   /***********************************************/
   /**************** 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=0.;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum=0.; /* 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=0;
     int i1, j1, jk, stepsize=0;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm=0, nhstepm=0;
     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=0., agebase=0.;
     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;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
     syscompilerinfo(0);
     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);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     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 --------*/
   
     /* Main 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(0);
   
     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 */
   
     /* Main ---------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=1+age+%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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
       model[strlen(model)-1]='\0';
     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=1+age+%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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     /* if(model[0]=='#'|| model[0]== '\0'){ */
     if(model[0]=='#'){
       printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
    'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
    'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
       if(mle != -1){
         printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
         exit(1);
       }
     }
     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,age*age makes 3*/
     else
       ncovmodel=2; /* Constant and age */
     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 chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You chose 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) { /* Main Wizard */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You chose 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 != jj)){
             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,jj);
           fprintf(ficlog,"%1d%1d",i,jj);
           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 */
   
     /*  Main data
      */
     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 */
     ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 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
                         */  
   
   /* Main decodemodel */
   
   
     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-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] is the maximum value of this jth covariate */
   
     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]);*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
     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
              * For k=4 covariates, h goes from 1 to 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
              *     h\k   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[12][3]=1; */
             /*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);
   
   
       
     /* Initialisation of ----------- 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);*/
   
   
     /* Initialisation of --------- 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);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* 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*/
     /* For mortality only */
     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]));
         fprintf(ficlog,"%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 mortality only */
     /* Standard maximisation */
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
       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; /* again, 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, Real Maximisation */
         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=1+age+%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("%12.7f ",p[jk]);
               fprintf(ficlog,"%12.7f ",p[jk]);
               fprintf(ficres,"%12.7f ",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);
       }
       printf("Parameters and 95%% confidence intervals\n");
       fprintf(ficlog, "Parameters, T and confidence intervals\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);
             for(j=1; j <=ncovmodel; j++){
               printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
               fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
           }
         }
       }
   
       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);
   
       /* Other stuffs, more or less useful */    
       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(ficlog,"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);
   
   
       /* Other results (useful)*/
   
   
       /*--------------- 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); */
         /*      } */
       }
    
       /* ------ Other prevalence ratios------------ */
   
       /* 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(ncodemaxwundef,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);
   #ifdef WIN32
      if (_chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n",path);
      if(_getcwd(pathcd,MAXLINE) > 0)
   #else
      if(chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n", path);
      if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
       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.1.45  
changed lines
  Added in v.1.193


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