Diff for /imach/src/imach.c between versions 1.36 and 1.190

version 1.36, 2002/03/29 15:27:27 version 1.190, 2015/05/05 08:51:13
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.190  2015/05/05 08:51:13  brouard
      Summary: Adding digits in output parameters (7 digits instead of 6)
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Fix 1+age+.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.189  2015/04/30 14:45:16  brouard
   case of a health survey which is our main interest) -2- at least a    Summary: 0.98q2
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.188  2015/04/30 08:27:53  brouard
   computed from the time spent in each health state according to a    *** empty log message ***
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.187  2015/04/29 09:11:15  brouard
   simplest model is the multinomial logistic model where pij is the    *** empty log message ***
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.186  2015/04/23 12:01:52  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: V1*age is working now, version 0.98q1
   '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    Some codes had been disabled in order to simplify and Vn*age was
   where the markup *Covariates have to be included here again* invites    working in the optimization phase, ie, giving correct MLE parameters,
   you to do it.  More covariates you add, slower the    but, as usual, outputs were not correct and program core dumped.
   convergence.  
     Revision 1.185  2015/03/11 13:26:42  brouard
   The advantage of this computer programme, compared to a simple    Summary: Inclusion of compile and links command line for Intel Compiler
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.184  2015/03/11 11:52:39  brouard
   intermediate interview, the information is lost, but taken into    Summary: Back from Windows 8. Intel Compiler
   account using an interpolation or extrapolation.    
     Revision 1.183  2015/03/10 20:34:32  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: 0.98q0, trying with directest, mnbrak fixed
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    We use directest instead of original Powell test; probably no
   states. This elementary transition (by month or quarter trimester,    incidence on the results, but better justifications;
   semester or year) is model as a multinomial logistic.  The hPx    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   matrix is simply the matrix product of nh*stepm elementary matrices    wrong results.
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.182  2015/02/12 08:19:57  brouard
     Summary: Trying to keep directest which seems simpler and more general
   Also this programme outputs the covariance matrix of the parameters but also    Author: Nicolas Brouard
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.181  2015/02/11 23:22:24  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Summary: Comments on Powell added
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Author:
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.180  2015/02/11 17:33:45  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.179  2015/01/04 09:57:06  brouard
      Summary: back to OS/X
 #include <math.h>  
 #include <stdio.h>    Revision 1.178  2015/01/04 09:35:48  brouard
 #include <stdlib.h>    *** empty log message ***
 #include <unistd.h>  
     Revision 1.177  2015/01/03 18:40:56  brouard
 #define MAXLINE 256    Summary: Still testing ilc32 on OSX
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.176  2015/01/03 16:45:04  brouard
 #define FILENAMELENGTH 80    *** empty log message ***
 /*#define DEBUG*/  
 #define windows    Revision 1.175  2015/01/03 16:33:42  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    *** empty log message ***
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.174  2015/01/03 16:15:49  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: Still in cross-compilation
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.173  2015/01/03 12:06:26  brouard
 #define NINTERVMAX 8    Summary: trying to detect cross-compilation
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.172  2014/12/27 12:07:47  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.171  2014/12/23 13:26:59  brouard
 #define AGESUP 130    Summary: Back from Visual C
 #define AGEBASE 40  
     Still problem with utsname.h on Windows
   
 int erreur; /* Error number */    Revision 1.170  2014/12/23 11:17:12  brouard
 int nvar;    Summary: Cleaning some \%% back to %%
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.169  2014/12/22 23:08:31  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Summary: 0.98p
 int popbased=0;  
     Outputs some informations on compiler used, OS etc. Testing on different platforms.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.168  2014/12/22 15:17:42  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    Summary: update
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.167  2014/12/22 13:50:56  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Summary: Testing uname and compiler version and if compiled 32 or 64
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Testing on Linux 64
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.166  2014/12/22 11:40:47  brouard
 FILE *ficgp,*ficresprob,*ficpop;    *** empty log message ***
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.165  2014/12/16 11:20:36  brouard
  FILE  *ficresvij;    Summary: After compiling on Visual C
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    * imach.c (Module): Merging 1.61 to 1.162
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.164  2014/12/16 10:52:11  brouard
 #define NR_END 1    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    * imach.c (Module): Merging 1.61 to 1.162
   
 #define NRANSI    Revision 1.163  2014/12/16 10:30:11  brouard
 #define ITMAX 200    * imach.c (Module): Merging 1.61 to 1.162
   
 #define TOL 2.0e-4    Revision 1.162  2014/09/25 11:43:39  brouard
     Summary: temporary backup 0.99!
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.1  2014/09/16 11:06:58  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Summary: With some code (wrong) for nlopt
   
 #define GOLD 1.618034    Author:
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.160  2014/09/02 09:24:05  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    *** empty log message ***
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.159  2014/09/01 10:34:10  brouard
 #define rint(a) floor(a+0.5)    Summary: WIN32
     Author: Brouard
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.158  2014/08/27 17:11:51  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    *** empty log message ***
   
 int imx;    Revision 1.157  2014/08/27 16:26:55  brouard
 int stepm;    Summary: Preparing windows Visual studio version
 /* Stepm, step in month: minimum step interpolation*/    Author: Brouard
   
 int estepm;    In order to compile on Visual studio, time.h is now correct and time_t
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
 int m,nb;    Trying to suppress #ifdef LINUX
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Add xdg-open for __linux in order to open default browser.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.156  2014/08/25 20:10:10  brouard
 double dateintmean=0;    *** empty log message ***
   
 double *weight;    Revision 1.155  2014/08/25 18:32:34  brouard
 int **s; /* Status */    Summary: New compile, minor changes
 double *agedc, **covar, idx;    Author: Brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.154  2014/06/20 17:32:08  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Summary: Outputs now all graphs of convergence to period prevalence
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.153  2014/06/20 16:45:46  brouard
 /**************** split *************************/    Summary: If 3 live state, convergence to period prevalence on same graph
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Author: Brouard
 {  
    char *s;                             /* pointer */    Revision 1.152  2014/06/18 17:54:09  brouard
    int  l1, l2;                         /* length counters */    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
    l1 = strlen( path );                 /* length of path */    Revision 1.151  2014/06/18 16:43:30  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    *** empty log message ***
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.150  2014/06/18 16:42:35  brouard
 #else    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
    s = strrchr( path, '/' );            /* find last / */    Author: brouard
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.149  2014/06/18 15:51:14  brouard
 #if     defined(__bsd__)                /* get current working directory */    Summary: Some fixes in parameter files errors
       extern char       *getwd( );    Author: Nicolas Brouard
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.148  2014/06/17 17:38:48  brouard
 #else    Summary: Nothing new
       extern char       *getcwd( );    Author: Brouard
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Just a new packaging for OS/X version 0.98nS
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.147  2014/06/16 10:33:11  brouard
       }    *** empty log message ***
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.146  2014/06/16 10:20:28  brouard
       s++;                              /* after this, the filename */    Summary: Merge
       l2 = strlen( s );                 /* length of filename */    Author: Brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Merge, before building revised version.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.145  2014/06/10 21:23:15  brouard
    }    Summary: Debugging with valgrind
    l1 = strlen( dirc );                 /* length of directory */    Author: Nicolas Brouard
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Lot of changes in order to output the results with some covariates
 #else    After the Edimburgh REVES conference 2014, it seems mandatory to
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    improve the code.
 #endif    No more memory valgrind error but a lot has to be done in order to
    s = strrchr( name, '.' );            /* find last / */    continue the work of splitting the code into subroutines.
    s++;    Also, decodemodel has been improved. Tricode is still not
    strcpy(ext,s);                       /* save extension */    optimal. nbcode should be improved. Documentation has been added in
    l1= strlen( name);    the source code.
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.143  2014/01/26 09:45:38  brouard
    finame[l1-l2]= 0;    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
    return( 0 );                         /* we're done */  
 }    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
 /******************************************/    Revision 1.142  2014/01/26 03:57:36  brouard
     Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 void replace(char *s, char*t)  
 {    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   int i;  
   int lg=20;    Revision 1.141  2014/01/26 02:42:01  brouard
   i=0;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.140  2011/09/02 10:37:54  brouard
     (s[i] = t[i]);    Summary: times.h is ok with mingw32 now.
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.139  2010/06/14 07:50:17  brouard
 }    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 int nbocc(char *s, char occ)  
 {    Revision 1.138  2010/04/30 18:19:40  brouard
   int i,j=0;    *** empty log message ***
   int lg=20;  
   i=0;    Revision 1.137  2010/04/29 18:11:38  brouard
   lg=strlen(s);    (Module): Checking covariates for more complex models
   for(i=0; i<= lg; i++) {    than V1+V2. A lot of change to be done. Unstable.
   if  (s[i] == occ ) j++;  
   }    Revision 1.136  2010/04/26 20:30:53  brouard
   return j;    (Module): merging some libgsl code. Fixing computation
 }    of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
 void cutv(char *u,char *v, char*t, char occ)    Some cleaning of code and comments added.
 {  
   int i,lg,j,p=0;    Revision 1.135  2009/10/29 15:33:14  brouard
   i=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<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.134  2009/10/29 13:18:53  brouard
   }    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
   lg=strlen(t);    Revision 1.133  2009/07/06 10:21:25  brouard
   for(j=0; j<p; j++) {    just nforces
     (u[j] = t[j]);  
   }    Revision 1.132  2009/07/06 08:22:05  brouard
      u[p]='\0';    Many tings
   
    for(j=0; j<= lg; j++) {    Revision 1.131  2009/06/20 16:22:47  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    Some dimensions resccaled
   }  
 }    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
 /********************** nrerror ********************/    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 void nrerror(char error_text[])  
 {    Revision 1.129  2007/08/31 13:49:27  lievre
   fprintf(stderr,"ERREUR ...\n");    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.128  2006/06/30 13:02:05  brouard
 }    (Module): Clarifications on computing e.j
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    Revision 1.127  2006/04/28 18:11:50  brouard
 {    (Module): Yes the sum of survivors was wrong since
   double *v;    imach-114 because nhstepm was no more computed in the age
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    loop. Now we define nhstepma in the age loop.
   if (!v) nrerror("allocation failure in vector");    (Module): In order to speed up (in case of numerous covariates) we
   return v-nl+NR_END;    compute health expectancies (without variances) in a first step
 }    and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
 /************************ free vector ******************/    computation.
 void free_vector(double*v, int nl, int nh)    In the future we should be able to stop the program is only health
 {    expectancies and graph are needed without standard deviations.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
 /************************ivector *******************************/    imach-114 because nhstepm was no more computed in the age
 int *ivector(long nl,long nh)    loop. Now we define nhstepma in the age loop.
 {    Version 0.98h
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.125  2006/04/04 15:20:31  lievre
   if (!v) nrerror("allocation failure in ivector");    Errors in calculation of health expectancies. Age was not initialized.
   return v-nl+NR_END;    Forecasting file added.
 }  
     Revision 1.124  2006/03/22 17:13:53  lievre
 /******************free ivector **************************/    Parameters are printed with %lf instead of %f (more numbers after the comma).
 void free_ivector(int *v, long nl, long nh)    The log-likelihood is printed in the log file
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.123  2006/03/20 10:52:43  brouard
 }    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    * imach.c (Module): Weights can have a decimal point as for
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    English (a comma might work with a correct LC_NUMERIC environment,
 {    otherwise the weight is truncated).
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Modification of warning when the covariates values are not 0 or
   int **m;    1.
      Version 0.98g
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.122  2006/03/20 09:45:41  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Weights can have a decimal point as for
   m += NR_END;    English (a comma might work with a correct LC_NUMERIC environment,
   m -= nrl;    otherwise the weight is truncated).
      Modification of warning when the covariates values are not 0 or
      1.
   /* allocate rows and set pointers to them */    Version 0.98g
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.121  2006/03/16 17:45:01  lievre
   m[nrl] += NR_END;    * imach.c (Module): Comments concerning covariates added
   m[nrl] -= ncl;  
      * imach.c (Module): refinements in the computation of lli if
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    status=-2 in order to have more reliable computation if stepm is
      not 1 month. Version 0.98f
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.120  2006/03/16 15:10:38  lievre
 }    (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 /****************** free_imatrix *************************/    not 1 month. Version 0.98f
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.119  2006/03/15 17:42:26  brouard
       long nch,ncl,nrh,nrl;    (Module): Bug if status = -2, the loglikelihood was
      /* free an int matrix allocated by imatrix() */    computed as likelihood omitting the logarithm. Version O.98e
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Revision 1.118  2006/03/14 18:20:07  brouard
   free((FREE_ARG) (m+nrl-NR_END));    (Module): varevsij Comments added explaining the second
 }    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /******************* matrix *******************************/    (Module): Function pstamp added
 double **matrix(long nrl, long nrh, long ncl, long nch)    (Module): Version 0.98d
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Revision 1.117  2006/03/14 17:16:22  brouard
   double **m;    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Function pstamp added
   m += NR_END;    (Module): Version 0.98d
   m -= nrl;  
     Revision 1.116  2006/03/06 10:29:27  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Variance-covariance wrong links and
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    varian-covariance of ej. is needed (Saito).
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.114  2006/02/26 12:57:58  brouard
 }    (Module): Some improvements in processing parameter
     filename with strsep.
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Revision 1.113  2006/02/24 14:20:24  brouard
 {    (Module): Memory leaks checks with valgrind and:
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    datafile was not closed, some imatrix were not freed and on matrix
   free((FREE_ARG)(m+nrl-NR_END));    allocation too.
 }  
     Revision 1.112  2006/01/30 09:55:26  brouard
 /******************* ma3x *******************************/    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    Revision 1.111  2006/01/25 20:38:18  brouard
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    (Module): Lots of cleaning and bugs added (Gompertz)
   double ***m;    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.110  2006/01/25 00:51:50  brouard
   m += NR_END;    (Module): Lots of cleaning and bugs added (Gompertz)
   m -= nrl;  
     Revision 1.109  2006/01/24 19:37:15  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Comments (lines starting with a #) are allowed in data.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.108  2006/01/19 18:05:42  lievre
   m[nrl] -= ncl;    Gnuplot problem appeared...
     To be fixed
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Revision 1.107  2006/01/19 16:20:37  brouard
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Test existence of gnuplot in imach path
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    Revision 1.106  2006/01/19 13:24:36  brouard
   m[nrl][ncl] -= nll;    Some cleaning and links added in html output
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    Revision 1.105  2006/01/05 20:23:19  lievre
      *** empty log message ***
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Revision 1.104  2005/09/30 16:11:43  lievre
     for (j=ncl+1; j<=nch; j++)    (Module): sump fixed, loop imx fixed, and simplifications.
       m[i][j]=m[i][j-1]+nlay;    (Module): If the status is missing at the last wave but we know
   }    that the person is alive, then we can code his/her status as -2
   return m;    (instead of missing=-1 in earlier versions) and his/her
 }    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
 /*************************free ma3x ************************/    the healthy state at last known wave). Version is 0.98
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    Revision 1.103  2005/09/30 15:54:49  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));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.102  2004/09/15 17:31:30  brouard
 }    Add the possibility to read data file including tab characters.
   
 /***************** f1dim *************************/    Revision 1.101  2004/09/15 10:38:38  brouard
 extern int ncom;    Fix on curr_time
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    Revision 1.100  2004/07/12 18:29:06  brouard
      Add version for Mac OS X. Just define UNIX in Makefile
 double f1dim(double x)  
 {    Revision 1.99  2004/06/05 08:57:40  brouard
   int j;    *** empty log message ***
   double f;  
   double *xt;    Revision 1.98  2004/05/16 15:05:56  brouard
      New version 0.97 . First attempt to estimate force of mortality
   xt=vector(1,ncom);    directly from the data i.e. without the need of knowing the health
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    state at each age, but using a Gompertz model: log u =a + b*age .
   f=(*nrfunc)(xt);    This is the basic analysis of mortality and should be done before any
   free_vector(xt,1,ncom);    other analysis, in order to test if the mortality estimated from the
   return f;    cross-longitudinal survey is different from the mortality estimated
 }    from other sources like vital statistic data.
   
 /*****************brent *************************/    The same imach parameter file can be used but the option for mle should be -3.
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {    Agnès, who wrote this part of the code, tried to keep most of the
   int iter;    former routines in order to include the new code within the former code.
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    The output is very simple: only an estimate of the intercept and of
   double ftemp;    the slope with 95% confident intervals.
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    Current limitations:
      A) Even if you enter covariates, i.e. with the
   a=(ax < cx ? ax : cx);    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   b=(ax > cx ? ax : cx);    B) There is no computation of Life Expectancy nor Life Table.
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    Revision 1.97  2004/02/20 13:25:42  lievre
   for (iter=1;iter<=ITMAX;iter++) {    Version 0.96d. Population forecasting command line is (temporarily)
     xm=0.5*(a+b);    suppressed.
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    Revision 1.96  2003/07/15 15:38:55  brouard
     printf(".");fflush(stdout);    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #ifdef DEBUG    rewritten within the same printf. Workaround: many printfs.
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    Revision 1.95  2003/07/08 07:54:34  brouard
 #endif    * imach.c (Repository):
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    (Repository): Using imachwizard code to output a more meaningful covariance
       *xmin=x;    matrix (cov(a12,c31) instead of numbers.
       return fx;  
     }    Revision 1.94  2003/06/27 13:00:02  brouard
     ftemp=fu;    Just cleaning
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    Revision 1.93  2003/06/25 16:33:55  brouard
       q=(x-v)*(fx-fw);    (Module): On windows (cygwin) function asctime_r doesn't
       p=(x-v)*q-(x-w)*r;    exist so I changed back to asctime which exists.
       q=2.0*(q-r);    (Module): Version 0.96b
       if (q > 0.0) p = -p;  
       q=fabs(q);    Revision 1.92  2003/06/25 16:30:45  brouard
       etemp=e;    (Module): On windows (cygwin) function asctime_r doesn't
       e=d;    exist so I changed back to asctime which exists.
       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 1.91  2003/06/25 15:30:29  brouard
       else {    * imach.c (Repository): Duplicated warning errors corrected.
         d=p/q;    (Repository): Elapsed time after each iteration is now output. It
         u=x+d;    helps to forecast when convergence will be reached. Elapsed time
         if (u-a < tol2 || b-u < tol2)    is stamped in powell.  We created a new html file for the graphs
           d=SIGN(tol1,xm-x);    concerning matrix of covariance. It has extension -cov.htm.
       }  
     } else {    Revision 1.90  2003/06/24 12:34:15  brouard
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    (Module): Some bugs corrected for windows. Also, when
     }    mle=-1 a template is output in file "or"mypar.txt with the design
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    of the covariance matrix to be input.
     fu=(*f)(u);  
     if (fu <= fx) {    Revision 1.89  2003/06/24 12:30:52  brouard
       if (u >= x) a=x; else b=x;    (Module): Some bugs corrected for windows. Also, when
       SHFT(v,w,x,u)    mle=-1 a template is output in file "or"mypar.txt with the design
         SHFT(fv,fw,fx,fu)    of the covariance matrix to be input.
         } else {  
           if (u < x) a=u; else b=u;    Revision 1.88  2003/06/23 17:54:56  brouard
           if (fu <= fw || w == x) {    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
             v=w;  
             w=u;    Revision 1.87  2003/06/18 12:26:01  brouard
             fv=fw;    Version 0.96
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {    Revision 1.86  2003/06/17 20:04:08  brouard
             v=u;    (Module): Change position of html and gnuplot routines and added
             fv=fu;    routine fileappend.
           }  
         }    Revision 1.85  2003/06/17 13:12:43  brouard
   }    * imach.c (Repository): Check when date of death was earlier that
   nrerror("Too many iterations in brent");    current date of interview. It may happen when the death was just
   *xmin=x;    prior to the death. In this case, dh was negative and likelihood
   return fx;    was wrong (infinity). We still send an "Error" but patch by
 }    assuming that the date of death was just one stepm after the
     interview.
 /****************** mnbrak ***********************/    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    memory allocation. But we also truncated to 8 characters (left
             double (*func)(double))    truncation)
 {    (Repository): No more line truncation errors.
   double ulim,u,r,q, dum;  
   double fu;    Revision 1.84  2003/06/13 21:44:43  brouard
      * imach.c (Repository): Replace "freqsummary" at a correct
   *fa=(*func)(*ax);    place. It differs from routine "prevalence" which may be called
   *fb=(*func)(*bx);    many times. Probs is memory consuming and must be used with
   if (*fb > *fa) {    parcimony.
     SHFT(dum,*ax,*bx,dum)    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       SHFT(dum,*fb,*fa,dum)  
       }    Revision 1.83  2003/06/10 13:39:11  lievre
   *cx=(*bx)+GOLD*(*bx-*ax);    *** empty log message ***
   *fc=(*func)(*cx);  
   while (*fb > *fc) {    Revision 1.82  2003/06/05 15:57:20  brouard
     r=(*bx-*ax)*(*fb-*fc);    Add log in  imach.c and  fullversion number is now printed.
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /*
     ulim=(*bx)+GLIMIT*(*cx-*bx);     Interpolated Markov Chain
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    Short summary of the programme:
     } else if ((*cx-u)*(u-ulim) > 0.0) {    
       fu=(*func)(u);    This program computes Healthy Life Expectancies from
       if (fu < *fc) {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    first survey ("cross") where individuals from different ages are
           SHFT(*fb,*fc,fu,(*func)(u))    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
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    second wave of interviews ("longitudinal") which measure each change
       u=ulim;    (if any) in individual health status.  Health expectancies are
       fu=(*func)(u);    computed from the time spent in each health state according to a
     } else {    model. More health states you consider, more time is necessary to reach the
       u=(*cx)+GOLD*(*cx-*bx);    Maximum Likelihood of the parameters involved in the model.  The
       fu=(*func)(u);    simplest model is the multinomial logistic model where pij is the
     }    probability to be observed in state j at the second wave
     SHFT(*ax,*bx,*cx,u)    conditional to be observed in state i at the first wave. Therefore
       SHFT(*fa,*fb,*fc,fu)    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       }    'age' is age and 'sex' is a covariate. If you want to have a more
 }    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 /*************** linmin ************************/    you to do it.  More covariates you add, slower the
     convergence.
 int ncom;  
 double *pcom,*xicom;    The advantage of this computer programme, compared to a simple
 double (*nrfunc)(double []);    multinomial logistic model, is clear when the delay between waves is not
      identical for each individual. Also, if a individual missed an
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    intermediate interview, the information is lost, but taken into
 {    account using an interpolation or extrapolation.  
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);    hPijx is the probability to be observed in state i at age x+h
   double f1dim(double x);    conditional to the observed state i at age x. The delay 'h' can be
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    split into an exact number (nh*stepm) of unobserved intermediate
               double *fc, double (*func)(double));    states. This elementary transition (by month, quarter,
   int j;    semester or year) is modelled as a multinomial logistic.  The hPx
   double xx,xmin,bx,ax;    matrix is simply the matrix product of nh*stepm elementary matrices
   double fx,fb,fa;    and the contribution of each individual to the likelihood is simply
      hPijx.
   ncom=n;  
   pcom=vector(1,n);    Also this programme outputs the covariance matrix of the parameters but also
   xicom=vector(1,n);    of the life expectancies. It also computes the period (stable) prevalence. 
   nrfunc=func;    
   for (j=1;j<=n;j++) {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     pcom[j]=p[j];             Institut national d'études démographiques, Paris.
     xicom[j]=xi[j];    This software have been partly granted by Euro-REVES, a concerted action
   }    from the European Union.
   ax=0.0;    It is copyrighted identically to a GNU software product, ie programme and
   xx=1.0;    software can be distributed freely for non commercial use. Latest version
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    can be accessed at http://euroreves.ined.fr/imach .
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #endif    
   for (j=1;j<=n;j++) {    **********************************************************************/
     xi[j] *= xmin;  /*
     p[j] += xi[j];    main
   }    read parameterfile
   free_vector(xicom,1,n);    read datafile
   free_vector(pcom,1,n);    concatwav
 }    freqsummary
     if (mle >= 1)
 /*************** powell ************************/      mlikeli
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    print results files
             double (*func)(double []))    if mle==1 
 {       computes hessian
   void linmin(double p[], double xi[], int n, double *fret,    read end of parameter file: agemin, agemax, bage, fage, estepm
               double (*func)(double []));        begin-prev-date,...
   int i,ibig,j;    open gnuplot file
   double del,t,*pt,*ptt,*xit;    open html file
   double fp,fptt;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   double *xits;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   pt=vector(1,n);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   ptt=vector(1,n);      freexexit2 possible for memory heap.
   xit=vector(1,n);  
   xits=vector(1,n);    h Pij x                         | pij_nom  ficrestpij
   *fret=(*func)(p);     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   for (j=1;j<=n;j++) pt[j]=p[j];         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   for (*iter=1;;++(*iter)) {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
     fp=(*fret);  
     ibig=0;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
     del=0.0;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
     for (i=1;i<=n;i++)     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       printf(" %d %.12f",i, p[i]);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
     printf("\n");  
     for (i=1;i<=n;i++) {    forecasting if prevfcast==1 prevforecast call prevalence()
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    health expectancies
       fptt=(*fret);    Variance-covariance of DFLE
 #ifdef DEBUG    prevalence()
       printf("fret=%lf \n",*fret);     movingaverage()
 #endif    varevsij() 
       printf("%d",i);fflush(stdout);    if popbased==1 varevsij(,popbased)
       linmin(p,xit,n,fret,func);    total life expectancies
       if (fabs(fptt-(*fret)) > del) {    Variance of period (stable) prevalence
         del=fabs(fptt-(*fret));   end
         ibig=i;  */
       }  
 #ifdef DEBUG  /* #define DEBUG */
       printf("%d %.12e",i,(*fret));  /* #define DEBUGBRENT */
       for (j=1;j<=n;j++) {  #define POWELL /* Instead of NLOPT */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
         printf(" x(%d)=%.12e",j,xit[j]);  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
       }  
       for(j=1;j<=n;j++)  #include <math.h>
         printf(" p=%.12e",p[j]);  #include <stdio.h>
       printf("\n");  #include <stdlib.h>
 #endif  #include <string.h>
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #ifdef _WIN32
 #ifdef DEBUG  #include <io.h>
       int k[2],l;  #include <windows.h>
       k[0]=1;  #include <tchar.h>
       k[1]=-1;  #else
       printf("Max: %.12e",(*func)(p));  #include <unistd.h>
       for (j=1;j<=n;j++)  #endif
         printf(" %.12e",p[j]);  
       printf("\n");  #include <limits.h>
       for(l=0;l<=1;l++) {  #include <sys/types.h>
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #if defined(__GNUC__)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #include <sys/utsname.h> /* Doesn't work on Windows */
         }  #endif
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  #include <sys/stat.h>
 #endif  #include <errno.h>
   /* extern int errno; */
   
       free_vector(xit,1,n);  /* #ifdef LINUX */
       free_vector(xits,1,n);  /* #include <time.h> */
       free_vector(ptt,1,n);  /* #include "timeval.h" */
       free_vector(pt,1,n);  /* #else */
       return;  /* #include <sys/time.h> */
     }  /* #endif */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  #include <time.h>
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  #ifdef GSL
       pt[j]=p[j];  #include <gsl/gsl_errno.h>
     }  #include <gsl/gsl_multimin.h>
     fptt=(*func)(ptt);  #endif
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  #ifdef NLOPT
         linmin(p,xit,n,fret,func);  #include <nlopt.h>
         for (j=1;j<=n;j++) {  typedef struct {
           xi[j][ibig]=xi[j][n];    double (* function)(double [] );
           xi[j][n]=xit[j];  } myfunc_data ;
         }  #endif
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /* #include <libintl.h> */
         for(j=1;j<=n;j++)  /* #define _(String) gettext (String) */
           printf(" %.12e",xit[j]);  
         printf("\n");  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
 #endif  
       }  #define GNUPLOTPROGRAM "gnuplot"
     }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   }  #define FILENAMELENGTH 132
 }  
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /**** Prevalence limit ****************/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
 {  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   /* 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 NINTERVMAX 8
   #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   int i, ii,j,k;  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   double min, max, maxmin, maxmax,sumnew=0.;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   double **matprod2();  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   double **out, cov[NCOVMAX], **pmij();  #define MAXN 20000
   double **newm;  #define YEARM 12. /**< Number of months per year */
   double agefin, delaymax=50 ; /* Max number of years to converge */  #define AGESUP 130
   #define AGEBASE 40
   for (ii=1;ii<=nlstate+ndeath;ii++)  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
     for (j=1;j<=nlstate+ndeath;j++){  #ifdef _WIN32
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #define DIRSEPARATOR '\\'
     }  #define CHARSEPARATOR "\\"
   #define ODIRSEPARATOR '/'
    cov[1]=1.;  #else
    #define DIRSEPARATOR '/'
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #define CHARSEPARATOR "/"
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #define ODIRSEPARATOR '\\'
     newm=savm;  #endif
     /* Covariates have to be included here again */  
      cov[2]=agefin;  /* $Id$ */
    /* $State$ */
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
         /*      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]]);*/  char fullversion[]="$Revision$ $Date$"; 
       }  char strstart[80];
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       for (k=1; k<=cptcovprod;k++)  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
   /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   int cptcovprodnoage=0; /**< Number of covariate products without age */   
     savm=oldm;  int cptcoveff=0; /* Total number of covariates to vary for printing results */
     oldm=newm;  int cptcov=0; /* Working variable */
     maxmax=0.;  int npar=NPARMAX;
     for(j=1;j<=nlstate;j++){  int nlstate=2; /* Number of live states */
       min=1.;  int ndeath=1; /* Number of dead states */
       max=0.;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       for(i=1; i<=nlstate; i++) {  int popbased=0;
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  int *wav; /* Number of waves for this individuual 0 is possible */
         prlim[i][j]= newm[i][j]/(1-sumnew);  int maxwav=0; /* Maxim number of waves */
         max=FMAX(max,prlim[i][j]);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
         min=FMIN(min,prlim[i][j]);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       }  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       maxmin=max-min;                     to the likelihood and the sum of weights (done by funcone)*/
       maxmax=FMAX(maxmax,maxmin);  int mle=1, weightopt=0;
     }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     if(maxmax < ftolpl){  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       return prlim;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   }  int countcallfunc=0;  /* Count the number of calls to func */
 }  double jmean=1; /* Mean space between 2 waves */
   double **matprod2(); /* test */
 /*************** transition probabilities ***************/  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /*FILE *fic ; */ /* Used in readdata only */
 {  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   double s1, s2;  FILE *ficlog, *ficrespow;
   /*double t34;*/  int globpr=0; /* Global variable for printing or not */
   int i,j,j1, nc, ii, jj;  double fretone; /* Only one call to likelihood */
   long ipmx=0; /* Number of contributions */
     for(i=1; i<= nlstate; i++){  double sw; /* Sum of weights */
     for(j=1; j<i;j++){  char filerespow[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         /*s2 += param[i][j][nc]*cov[nc];*/  FILE *ficresilk;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  FILE *ficresprobmorprev;
       }  FILE *fichtm, *fichtmcov; /* Html File */
       ps[i][j]=s2;  FILE *ficreseij;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char filerese[FILENAMELENGTH];
     }  FILE *ficresstdeij;
     for(j=i+1; j<=nlstate+ndeath;j++){  char fileresstde[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  FILE *ficrescveij;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char filerescve[FILENAMELENGTH];
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  FILE  *ficresvij;
       }  char fileresv[FILENAMELENGTH];
       ps[i][j]=s2;  FILE  *ficresvpl;
     }  char fileresvpl[FILENAMELENGTH];
   }  char title[MAXLINE];
     /*ps[3][2]=1;*/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   for(i=1; i<= nlstate; i++){  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
      s1=0;  char command[FILENAMELENGTH];
     for(j=1; j<i; j++)  int  outcmd=0;
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  char filelog[FILENAMELENGTH]; /* Log file */
     for(j=1; j<i; j++)  char filerest[FILENAMELENGTH];
       ps[i][j]= exp(ps[i][j])*ps[i][i];  char fileregp[FILENAMELENGTH];
     for(j=i+1; j<=nlstate+ndeath; j++)  char popfile[FILENAMELENGTH];
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   } /* end i */  
   /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  /* struct timezone tzp; */
     for(jj=1; jj<= nlstate+ndeath; jj++){  /* extern int gettimeofday(); */
       ps[ii][jj]=0;  struct tm tml, *gmtime(), *localtime();
       ps[ii][ii]=1;  
     }  extern time_t time();
   }  
   struct tm start_time, end_time, curr_time, last_time, forecast_time;
   time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  struct tm tm;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  char strcurr[80], strfor[80];
    }  
     printf("\n ");  char *endptr;
     }  long lval;
     printf("\n ");printf("%lf ",cov[2]);*/  double dval;
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  #define NR_END 1
   goto end;*/  #define FREE_ARG char*
     return ps;  #define FTOL 1.0e-10
 }  
   #define NRANSI 
 /**************** Product of 2 matrices ******************/  #define ITMAX 200 
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  #define TOL 2.0e-4 
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  #define CGOLD 0.3819660 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  #define ZEPS 1.0e-10 
   /* in, b, out are matrice of pointers which should have been initialized  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */  #define GOLD 1.618034 
   long i, j, k;  #define GLIMIT 100.0 
   for(i=nrl; i<= nrh; i++)  #define TINY 1.0e-20 
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  static double maxarg1,maxarg2;
         out[i][k] +=in[i][j]*b[j][k];  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   return out;    
 }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
 /************* Higher Matrix Product ***************/  #define mytinydouble 1.0e-16
   /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
 {  /* static double dsqrarg; */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
      duration (i.e. until  static double sqrarg;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
      (typically every 2 years instead of every month which is too big).  int agegomp= AGEGOMP;
      Model is determined by parameters x and covariates have to be  
      included manually here.  int imx; 
   int stepm=1;
      */  /* Stepm, step in month: minimum step interpolation*/
   
   int i, j, d, h, k;  int estepm;
   double **out, cov[NCOVMAX];  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   double **newm;  
   int m,nb;
   /* Hstepm could be zero and should return the unit matrix */  long *num;
   for (i=1;i<=nlstate+ndeath;i++)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     for (j=1;j<=nlstate+ndeath;j++){  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       oldm[i][j]=(i==j ? 1.0 : 0.0);  double **pmmij, ***probs;
       po[i][j][0]=(i==j ? 1.0 : 0.0);  double *ageexmed,*agecens;
     }  double dateintmean=0;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  double *weight;
     for(d=1; d <=hstepm; d++){  int **s; /* Status */
       newm=savm;  double *agedc;
       /* Covariates have to be included here again */  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       cov[1]=1.;                    * covar=matrix(0,NCOVMAX,1,n); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double  idx; 
       for (k=1; k<=cptcovage;k++)  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int *Ndum; /** Freq of modality (tricode */
       for (k=1; k<=cptcovprod;k++)  int **codtab; /**< codtab=imatrix(1,100,1,10); */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *lsurv, *lpop, *tpop;
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  double ftolhess; /**< Tolerance for computing hessian */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  /**************** split *************************/
       savm=oldm;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       oldm=newm;  {
     }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     for(i=1; i<=nlstate+ndeath; i++)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       for(j=1;j<=nlstate+ndeath;j++) {    */ 
         po[i][j][h]=newm[i][j];    char  *ss;                            /* pointer */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    int   l1=0, l2=0;                             /* length counters */
          */  
       }    l1 = strlen(path );                   /* length of path */
   } /* end h */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   return po;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /*************** log-likelihood *************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 double func( double *x)      /* get current working directory */
 {      /*    extern  char* getcwd ( char *buf , int len);*/
   int i, ii, j, k, mi, d, kk;  #ifdef WIN32
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
   double **out;  #else
   double sw; /* Sum of weights */          if (getcwd(dirc, FILENAME_MAX) == NULL) {
   double lli; /* Individual log likelihood */  #endif
   long ipmx;        return( GLOCK_ERROR_GETCWD );
   /*extern weight */      }
   /* We are differentiating ll according to initial status */      /* got dirc from getcwd*/
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      printf(" DIRC = %s \n",dirc);
   /*for(i=1;i<imx;i++)    } else {                              /* strip direcotry from path */
     printf(" %d\n",s[4][i]);      ss++;                               /* after this, the filename */
   */      l2 = strlen( ss );                  /* length of filename */
   cov[1]=1.;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
   for(k=1; k<=nlstate; k++) ll[k]=0.;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      dirc[l1-l2] = '\0';                 /* add zero */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      printf(" DIRC2 = %s \n",dirc);
     for(mi=1; mi<= wav[i]-1; mi++){    }
       for (ii=1;ii<=nlstate+ndeath;ii++)    /* We add a separator at the end of dirc if not exists */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    l1 = strlen( dirc );                  /* length of directory */
       for(d=0; d<dh[mi][i]; d++){    if( dirc[l1-1] != DIRSEPARATOR ){
         newm=savm;      dirc[l1] =  DIRSEPARATOR;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      dirc[l1+1] = 0; 
         for (kk=1; kk<=cptcovage;kk++) {      printf(" DIRC3 = %s \n",dirc);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    }
         }    ss = strrchr( name, '.' );            /* find last / */
            if (ss >0){
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      ss++;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      strcpy(ext,ss);                     /* save extension */
         savm=oldm;      l1= strlen( name);
         oldm=newm;      l2= strlen(ss)+1;
              strncpy( finame, name, l1-l2);
              finame[l1-l2]= 0;
       } /* end mult */    }
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    return( 0 );                          /* we're done */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  }
       ipmx +=1;  
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  /******************************************/
     } /* end of wave */  
   } /* end of individual */  void replace_back_to_slash(char *s, char*t)
   {
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    int i;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    int lg=0;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    i=0;
   return -l;    lg=strlen(t);
 }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /*********** Maximum Likelihood Estimation ***************/    }
   }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  char *trimbb(char *out, char *in)
   int i,j, iter;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   double **xi,*delti;    char *s;
   double fret;    s=out;
   xi=matrix(1,npar,1,npar);    while (*in != '\0'){
   for (i=1;i<=npar;i++)      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     for (j=1;j<=npar;j++)        in++;
       xi[i][j]=(i==j ? 1.0 : 0.0);      }
   printf("Powell\n");      *out++ = *in++;
   powell(p,xi,npar,ftol,&iter,&fret,func);    }
     *out='\0';
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    return s;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  }
   
 }  /* char *substrchaine(char *out, char *in, char *chain) */
   /* { */
 /**** Computes Hessian and covariance matrix ***/  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*   char *s, *t; */
 {  /*   t=in;s=out; */
   double  **a,**y,*x,pd;  /*   while ((*in != *chain) && (*in != '\0')){ */
   double **hess;  /*     *out++ = *in++; */
   int i, j,jk;  /*   } */
   int *indx;  
   /*   /\* *in matches *chain *\/ */
   double hessii(double p[], double delta, int theta, double delti[]);  /*   while ((*in++ == *chain++) && (*in != '\0')){ */
   double hessij(double p[], double delti[], int i, int j);  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  /*   } */
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /*   in--; chain--; */
   /*   while ( (*in != '\0')){ */
   hess=matrix(1,npar,1,npar);  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*     *out++ = *in++; */
   printf("\nCalculation of the hessian matrix. Wait...\n");  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   for (i=1;i<=npar;i++){  /*   } */
     printf("%d",i);fflush(stdout);  /*   *out='\0'; */
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*   out=s; */
     /*printf(" %f ",p[i]);*/  /*   return out; */
     /*printf(" %lf ",hess[i][i]);*/  /* } */
   }  char *substrchaine(char *out, char *in, char *chain)
    {
   for (i=1;i<=npar;i++) {    /* Substract chain 'chain' from 'in', return and output 'out' */
     for (j=1;j<=npar;j++)  {    /* in="V1+V1*age+age*age+V2", chain="age*age" */
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);    char *strloc;
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];        strcpy (out, in); 
         /*printf(" %lf ",hess[i][j]);*/    strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
       }    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
     }    if(strloc != NULL){ 
   }      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
   printf("\n");      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
       /* strcpy (strloc, strloc +strlen(chain));*/
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    }
      printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
   a=matrix(1,npar,1,npar);    return out;
   y=matrix(1,npar,1,npar);  }
   x=vector(1,npar);  
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)  char *cutl(char *blocc, char *alocc, char *in, char occ)
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  {
   ludcmp(a,npar,indx,&pd);    /* 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')
   for (j=1;j<=npar;j++) {       gives blocc="abcdef" and alocc="ghi2j".
     for (i=1;i<=npar;i++) x[i]=0;       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     x[j]=1;    */
     lubksb(a,npar,indx,x);    char *s, *t;
     for (i=1;i<=npar;i++){    t=in;s=in;
       matcov[i][j]=x[i];    while ((*in != occ) && (*in != '\0')){
     }      *alocc++ = *in++;
   }    }
     if( *in == occ){
   printf("\n#Hessian matrix#\n");      *(alocc)='\0';
   for (i=1;i<=npar;i++) {      s=++in;
     for (j=1;j<=npar;j++) {    }
       printf("%.3e ",hess[i][j]);   
     }    if (s == t) {/* occ not found */
     printf("\n");      *(alocc-(in-s))='\0';
   }      in=s;
     }
   /* Recompute Inverse */    while ( *in != '\0'){
   for (i=1;i<=npar;i++)      *blocc++ = *in++;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    }
   ludcmp(a,npar,indx,&pd);  
     *blocc='\0';
   /*  printf("\n#Hessian matrix recomputed#\n");    return t;
   }
   for (j=1;j<=npar;j++) {  char *cutv(char *blocc, char *alocc, char *in, char occ)
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
     lubksb(a,npar,indx,x);       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     for (i=1;i<=npar;i++){       gives blocc="abcdef2ghi" and alocc="j".
       y[i][j]=x[i];       If occ is not found blocc is null and alocc is equal to in. Returns alocc
       printf("%.3e ",y[i][j]);    */
     }    char *s, *t;
     printf("\n");    t=in;s=in;
   }    while (*in != '\0'){
   */      while( *in == occ){
         *blocc++ = *in++;
   free_matrix(a,1,npar,1,npar);        s=in;
   free_matrix(y,1,npar,1,npar);      }
   free_vector(x,1,npar);      *blocc++ = *in++;
   free_ivector(indx,1,npar);    }
   free_matrix(hess,1,npar,1,npar);    if (s == t) /* occ not found */
       *(blocc-(in-s))='\0';
     else
 }      *(blocc-(in-s)-1)='\0';
     in=s;
 /*************** hessian matrix ****************/    while ( *in != '\0'){
 double hessii( double x[], double delta, int theta, double delti[])      *alocc++ = *in++;
 {    }
   int i;  
   int l=1, lmax=20;    *alocc='\0';
   double k1,k2;    return s;
   double p2[NPARMAX+1];  }
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  int nbocc(char *s, char occ)
   double fx;  {
   int k=0,kmax=10;    int i,j=0;
   double l1;    int lg=20;
     i=0;
   fx=func(x);    lg=strlen(s);
   for (i=1;i<=npar;i++) p2[i]=x[i];    for(i=0; i<= lg; i++) {
   for(l=0 ; l <=lmax; l++){    if  (s[i] == occ ) j++;
     l1=pow(10,l);    }
     delts=delt;    return j;
     for(k=1 ; k <kmax; k=k+1){  }
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  /* void cutv(char *u,char *v, char*t, char occ) */
       k1=func(p2)-fx;  /* { */
       p2[theta]=x[theta]-delt;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       k2=func(p2)-fx;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
       /*res= (k1-2.0*fx+k2)/delt/delt; */  /*      gives u="abcdef2ghi" and v="j" *\/ */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  /*   int i,lg,j,p=0; */
        /*   i=0; */
 #ifdef DEBUG  /*   lg=strlen(t); */
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  /*   for(j=0; j<=lg-1; j++) { */
 #endif  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  /*   } */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;  /*   for(j=0; j<p; j++) { */
       }  /*     (u[j] = t[j]); */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  /*   } */
         k=kmax; l=lmax*10.;  /*      u[p]='\0'; */
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  /*    for(j=0; j<= lg; j++) { */
         delts=delt;  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       }  /*   } */
     }  /* } */
   }  
   delti[theta]=delts;  #ifdef _WIN32
   return res;  char * strsep(char **pp, const char *delim)
    {
 }    char *p, *q;
            
 double hessij( double x[], double delti[], int thetai,int thetaj)    if ((p = *pp) == NULL)
 {      return 0;
   int i;    if ((q = strpbrk (p, delim)) != NULL)
   int l=1, l1, lmax=20;    {
   double k1,k2,k3,k4,res,fx;      *pp = q + 1;
   double p2[NPARMAX+1];      *q = '\0';
   int k;    }
     else
   fx=func(x);      *pp = 0;
   for (k=1; k<=2; k++) {    return p;
     for (i=1;i<=npar;i++) p2[i]=x[i];  }
     p2[thetai]=x[thetai]+delti[thetai]/k;  #endif
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;  /********************** nrerror ********************/
    
     p2[thetai]=x[thetai]+delti[thetai]/k;  void nrerror(char error_text[])
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  {
     k2=func(p2)-fx;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
     p2[thetai]=x[thetai]-delti[thetai]/k;    exit(EXIT_FAILURE);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  }
     k3=func(p2)-fx;  /*********************** vector *******************/
    double *vector(int nl, int nh)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double *v;
     k4=func(p2)-fx;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    if (!v) nrerror("allocation failure in vector");
 #ifdef DEBUG    return v-nl+NR_END;
     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  
   }  /************************ free vector ******************/
   return res;  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /************** Inverse of matrix **************/  }
 void ludcmp(double **a, int n, int *indx, double *d)  
 {  /************************ivector *******************************/
   int i,imax,j,k;  int *ivector(long nl,long nh)
   double big,dum,sum,temp;  {
   double *vv;    int *v;
      v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   vv=vector(1,n);    if (!v) nrerror("allocation failure in ivector");
   *d=1.0;    return v-nl+NR_END;
   for (i=1;i<=n;i++) {  }
     big=0.0;  
     for (j=1;j<=n;j++)  /******************free ivector **************************/
       if ((temp=fabs(a[i][j])) > big) big=temp;  void free_ivector(int *v, long nl, long nh)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  {
     vv[i]=1.0/big;    free((FREE_ARG)(v+nl-NR_END));
   }  }
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {  /************************lvector *******************************/
       sum=a[i][j];  long *lvector(long nl,long nh)
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  {
       a[i][j]=sum;    long *v;
     }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     big=0.0;    if (!v) nrerror("allocation failure in ivector");
     for (i=j;i<=n;i++) {    return v-nl+NR_END;
       sum=a[i][j];  }
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  /******************free lvector **************************/
       a[i][j]=sum;  void free_lvector(long *v, long nl, long nh)
       if ( (dum=vv[i]*fabs(sum)) >= big) {  {
         big=dum;    free((FREE_ARG)(v+nl-NR_END));
         imax=i;  }
       }  
     }  /******************* imatrix *******************************/
     if (j != imax) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       for (k=1;k<=n;k++) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         dum=a[imax][k];  { 
         a[imax][k]=a[j][k];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         a[j][k]=dum;    int **m; 
       }    
       *d = -(*d);    /* allocate pointers to rows */ 
       vv[imax]=vv[j];    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     indx[j]=imax;    m += NR_END; 
     if (a[j][j] == 0.0) a[j][j]=TINY;    m -= nrl; 
     if (j != n) {    
       dum=1.0/(a[j][j]);    
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    /* allocate rows and set pointers to them */ 
     }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   free_vector(vv,1,n);  /* Doesn't work */    m[nrl] += NR_END; 
 ;    m[nrl] -= ncl; 
 }    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 void lubksb(double **a, int n, int *indx, double b[])    
 {    /* return pointer to array of pointers to rows */ 
   int i,ii=0,ip,j;    return m; 
   double sum;  } 
    
   for (i=1;i<=n;i++) {  /****************** free_imatrix *************************/
     ip=indx[i];  void free_imatrix(m,nrl,nrh,ncl,nch)
     sum=b[ip];        int **m;
     b[ip]=b[i];        long nch,ncl,nrh,nrl; 
     if (ii)       /* free an int matrix allocated by imatrix() */ 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  { 
     else if (sum) ii=i;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     b[i]=sum;    free((FREE_ARG) (m+nrl-NR_END)); 
   }  } 
   for (i=n;i>=1;i--) {  
     sum=b[i];  /******************* matrix *******************************/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  double **matrix(long nrl, long nrh, long ncl, long nch)
     b[i]=sum/a[i][i];  {
   }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /************ Frequencies ********************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 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)    if (!m) nrerror("allocation failure 1 in matrix()");
 {  /* Some frequencies */    m += NR_END;
      m -= nrl;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double *pp;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double pos, k2, dateintsum=0,k2cpt=0;    m[nrl] += NR_END;
   FILE *ficresp;    m[nrl] -= ncl;
   char fileresp[FILENAMELENGTH];  
      for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   pp=vector(1,nlstate);    return m;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   strcpy(fileresp,"p");  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   strcat(fileresp,fileres);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   if((ficresp=fopen(fileresp,"w"))==NULL) {     */
     printf("Problem with prevalence resultfile: %s\n", fileresp);  }
     exit(0);  
   }  /*************************free matrix ************************/
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   j1=0;  {
      free((FREE_ARG)(m[nrl]+ncl-NR_END));
   j=cptcoveff;    free((FREE_ARG)(m+nrl-NR_END));
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
    
   for(k1=1; k1<=j;k1++){  /******************* ma3x *******************************/
     for(i1=1; i1<=ncodemax[k1];i1++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       j1++;  {
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         scanf("%d", i);*/    double ***m;
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           for(m=agemin; m <= agemax+3; m++)    if (!m) nrerror("allocation failure 1 in matrix()");
             freq[i][jk][m]=0;    m += NR_END;
          m -= nrl;
       dateintsum=0;  
       k2cpt=0;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for (i=1; i<=imx; i++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         bool=1;    m[nrl] += NR_END;
         if  (cptcovn>0) {    m[nrl] -= ncl;
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
               bool=0;  
         }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         if (bool==1) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
           for(m=firstpass; m<=lastpass; m++){    m[nrl][ncl] += NR_END;
             k2=anint[m][i]+(mint[m][i]/12.);    m[nrl][ncl] -= nll;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    for (j=ncl+1; j<=nch; j++) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      m[nrl][j]=m[nrl][j-1]+nlay;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    
               if (m<lastpass) {    for (i=nrl+1; i<=nrh; i++) {
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      for (j=ncl+1; j<=nch; j++) 
               }        m[i][j]=m[i][j-1]+nlay;
                  }
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    return m; 
                 dateintsum=dateintsum+k2;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
                 k2cpt++;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
               }    */
             }  }
           }  
         }  /*************************free ma3x ************************/
       }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
          {
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
       if  (cptcovn>0) {    free((FREE_ARG)(m+nrl-NR_END));
         fprintf(ficresp, "\n#********** Variable ");  }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresp, "**********\n#");  /*************** function subdirf ***********/
       }  char *subdirf(char fileres[])
       for(i=1; i<=nlstate;i++)  {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    /* Caution optionfilefiname is hidden */
       fprintf(ficresp, "\n");    strcpy(tmpout,optionfilefiname);
          strcat(tmpout,"/"); /* Add to the right */
       for(i=(int)agemin; i <= (int)agemax+3; i++){    strcat(tmpout,fileres);
         if(i==(int)agemax+3)    return tmpout;
           printf("Total");  }
         else  
           printf("Age %d", i);  /*************** function subdirf2 ***********/
         for(jk=1; jk <=nlstate ; jk++){  char *subdirf2(char fileres[], char *preop)
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  {
             pp[jk] += freq[jk][m][i];    
         }    /* Caution optionfilefiname is hidden */
         for(jk=1; jk <=nlstate ; jk++){    strcpy(tmpout,optionfilefiname);
           for(m=-1, pos=0; m <=0 ; m++)    strcat(tmpout,"/");
             pos += freq[jk][m][i];    strcat(tmpout,preop);
           if(pp[jk]>=1.e-10)    strcat(tmpout,fileres);
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    return tmpout;
           else  }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
         }  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
         for(jk=1; jk <=nlstate ; jk++){  {
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    
             pp[jk] += freq[jk][m][i];    /* Caution optionfilefiname is hidden */
         }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
         for(jk=1,pos=0; jk <=nlstate ; jk++)    strcat(tmpout,preop);
           pos += pp[jk];    strcat(tmpout,preop2);
         for(jk=1; jk <=nlstate ; jk++){    strcat(tmpout,fileres);
           if(pos>=1.e-5)    return tmpout;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  }
           else  
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  char *asc_diff_time(long time_sec, char ascdiff[])
           if( i <= (int) agemax){  {
             if(pos>=1.e-5){    long sec_left, days, hours, minutes;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    days = (time_sec) / (60*60*24);
               probs[i][jk][j1]= pp[jk]/pos;    sec_left = (time_sec) % (60*60*24);
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    hours = (sec_left) / (60*60) ;
             }    sec_left = (sec_left) %(60*60);
             else    minutes = (sec_left) /60;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    sec_left = (sec_left) % (60);
           }    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
         }    return ascdiff;
          }
         for(jk=-1; jk <=nlstate+ndeath; jk++)  
           for(m=-1; m <=nlstate+ndeath; m++)  /***************** f1dim *************************/
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  extern int ncom; 
         if(i <= (int) agemax)  extern double *pcom,*xicom;
           fprintf(ficresp,"\n");  extern double (*nrfunc)(double []); 
         printf("\n");   
       }  double f1dim(double x) 
     }  { 
   }    int j; 
   dateintmean=dateintsum/k2cpt;    double f;
      double *xt; 
   fclose(ficresp);   
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    xt=vector(1,ncom); 
   free_vector(pp,1,nlstate);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
      f=(*nrfunc)(xt); 
   /* End of Freq */    free_vector(xt,1,ncom); 
 }    return f; 
   } 
 /************ Prevalence ********************/  
 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)  /*****************brent *************************/
 {  /* Some frequencies */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
    {
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
   double ***freq; /* Frequencies */     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
   double *pp;     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
   double pos, k2;     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
      * returned function value. 
   pp=vector(1,nlstate);    */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int iter; 
      double a,b,d,etemp;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double fu=0,fv,fw,fx;
   j1=0;    double ftemp=0.;
      double p,q,r,tol1,tol2,u,v,w,x,xm; 
   j=cptcoveff;    double e=0.0; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}   
      a=(ax < cx ? ax : cx); 
  for(k1=1; k1<=j;k1++){    b=(ax > cx ? ax : cx); 
     for(i1=1; i1<=ncodemax[k1];i1++){    x=w=v=bx; 
       j1++;    fw=fv=fx=(*f)(x); 
      for (iter=1;iter<=ITMAX;iter++) { 
       for (i=-1; i<=nlstate+ndeath; i++)        xm=0.5*(a+b); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
           for(m=agemin; m <= agemax+3; m++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
             freq[i][jk][m]=0;      printf(".");fflush(stdout);
            fprintf(ficlog,".");fflush(ficlog);
       for (i=1; i<=imx; i++) {  #ifdef DEBUGBRENT
         bool=1;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         if  (cptcovn>0) {      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
           for (z1=1; z1<=cptcoveff; z1++)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  #endif
               bool=0;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         }        *xmin=x; 
         if (bool==1) {        return fx; 
           for(m=firstpass; m<=lastpass; m++){      } 
             k2=anint[m][i]+(mint[m][i]/12.);      ftemp=fu;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      if (fabs(e) > tol1) { 
               if(agev[m][i]==0) agev[m][i]=agemax+1;        r=(x-w)*(fx-fv); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;        q=(x-v)*(fx-fw); 
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        p=(x-v)*q-(x-w)*r; 
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */        q=2.0*(q-r); 
             }        if (q > 0.0) p = -p; 
           }        q=fabs(q); 
         }        etemp=e; 
       }        e=d; 
         for(i=(int)agemin; i <= (int)agemax+3; i++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           for(jk=1; jk <=nlstate ; jk++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        else { 
               pp[jk] += freq[jk][m][i];          d=p/q; 
           }          u=x+d; 
           for(jk=1; jk <=nlstate ; jk++){          if (u-a < tol2 || b-u < tol2) 
             for(m=-1, pos=0; m <=0 ; m++)            d=SIGN(tol1,xm-x); 
             pos += freq[jk][m][i];        } 
         }      } else { 
                d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          for(jk=1; jk <=nlstate ; jk++){      } 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
              pp[jk] += freq[jk][m][i];      fu=(*f)(u); 
          }      if (fu <= fx) { 
                  if (u >= x) a=x; else b=x; 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        SHFT(v,w,x,u) 
         SHFT(fv,fw,fx,fu) 
          for(jk=1; jk <=nlstate ; jk++){                } else { 
            if( i <= (int) agemax){        if (u < x) a=u; else b=u; 
              if(pos>=1.e-5){        if (fu <= fw || w == x) { 
                probs[i][jk][j1]= pp[jk]/pos;          v=w; 
              }          w=u; 
            }          fv=fw; 
          }          fw=fu; 
                  } else if (fu <= fv || v == x || v == w) { 
         }          v=u; 
     }          fv=fu; 
   }        } 
        } 
      } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    nrerror("Too many iterations in brent"); 
   free_vector(pp,1,nlstate);    *xmin=x; 
      return fx; 
 }  /* End of Freq */  } 
   
 /************* Waves Concatenation ***************/  /****************** mnbrak ***********************/
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 {              double (*func)(double)) 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
      Death is a valid wave (if date is known).  the downhill direction (defined by the function as evaluated at the initial points) and returns
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
      and mw[mi+1][i]. dh depends on stepm.     */
      */    double ulim,u,r,q, dum;
     double fu; 
   int i, mi, m;  
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    double scale=10.;
      double sum=0., jmean=0.;*/    int iterscale=0;
   
   int j, k=0,jk, ju, jl;    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
   double sum=0.;    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
   jmin=1e+5;  
   jmax=-1;  
   jmean=0.;    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
   for(i=1; i<=imx; i++){    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
     mi=0;    /*   *bx = *ax - (*ax - *bx)/scale; */
     m=firstpass;    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
     while(s[m][i] <= nlstate){    /* } */
       if(s[m][i]>=1)  
         mw[++mi][i]=m;    if (*fb > *fa) { 
       if(m >=lastpass)      SHFT(dum,*ax,*bx,dum) 
         break;      SHFT(dum,*fb,*fa,dum) 
       else    } 
         m++;    *cx=(*bx)+GOLD*(*bx-*ax); 
     }/* end while */    *fc=(*func)(*cx); 
     if (s[m][i] > nlstate){  #ifdef DEBUG
       mi++;     /* Death is another wave */    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
       /* if(mi==0)  never been interviewed correctly before death */    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
          /* Only death is a correct wave */  #endif
       mw[mi][i]=m;    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
     }      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
     wav[i]=mi;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     if(mi==0)        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
   }      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
         fu=(*func)(u); 
   for(i=1; i<=imx; i++){  #ifdef DEBUG
     for(mi=1; mi<wav[i];mi++){        /* f(x)=A(x-u)**2+f(u) */
       if (stepm <=0)        double A, fparabu; 
         dh[mi][i]=1;        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
       else{        fparabu= *fa - A*(*ax-u)*(*ax-u);
         if (s[mw[mi+1][i]][i] > nlstate) {        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
           if (agedc[i] < 2*AGESUP) {        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);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        /* And thus,it can be that fu > *fc even if fparabu < *fc */
           if(j==0) j=1;  /* Survives at least one month after exam */        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
           k=k+1;          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
           if (j >= jmax) jmax=j;        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
           if (j <= jmin) jmin=j;  #endif 
           sum=sum+j;  #ifdef MNBRAKORIGINAL
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  #else
           }        if (fu > *fc) {
         }  #ifdef DEBUG
         else{        printf("mnbrak4  fu > fc \n");
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        fprintf(ficlog, "mnbrak4 fu > fc\n");
           k=k+1;  #endif
           if (j >= jmax) jmax=j;          /* 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 *\/  */
           else if (j <= jmin)jmin=j;          /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          dum=u; /* Shifting c and u */
           sum=sum+j;          u = *cx;
         }          *cx = dum;
         jk= j/stepm;          dum = fu;
         jl= j -jk*stepm;          fu = *fc;
         ju= j -(jk+1)*stepm;          *fc =dum;
         if(jl <= -ju)        } else { /* end */
           dh[mi][i]=jk;  #ifdef DEBUG
         else        printf("mnbrak3  fu < fc \n");
           dh[mi][i]=jk+1;        fprintf(ficlog, "mnbrak3 fu < fc\n");
         if(dh[mi][i]==0)  #endif
           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;
  }        }
 /*********** Tricode ****************************/  #endif
 void tricode(int *Tvar, int **nbcode, int imx)      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
 {  #ifdef DEBUG
   int Ndum[20],ij=1, k, j, i;        printf("mnbrak2  u after c but before ulim\n");
   int cptcode=0;        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
   cptcoveff=0;  #endif
          fu=(*func)(u); 
   for (k=0; k<19; k++) Ndum[k]=0;        if (fu < *fc) { 
   for (k=1; k<=7; k++) ncodemax[k]=0;  #ifdef DEBUG
         printf("mnbrak2  u after c but before ulim AND fu < fc\n");
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
     for (i=1; i<=imx; i++) {  #endif
       ij=(int)(covar[Tvar[j]][i]);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       Ndum[ij]++;          SHFT(*fb,*fc,fu,(*func)(u)) 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        } 
       if (ij > cptcode) cptcode=ij;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
     }  #ifdef DEBUG
         printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
     for (i=0; i<=cptcode; i++) {        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
       if(Ndum[i]!=0) ncodemax[j]++;  #endif
     }        u=ulim; 
     ij=1;        fu=(*func)(u); 
       } else { /* u could be left to b (if r > q parabola has a maximum) */
   #ifdef DEBUG
     for (i=1; i<=ncodemax[j]; i++) {        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
       for (k=0; k<=19; k++) {        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
         if (Ndum[k] != 0) {  #endif
           nbcode[Tvar[j]][ij]=k;        u=(*cx)+GOLD*(*cx-*bx); 
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/        fu=(*func)(u); 
           ij++;      } /* end tests */
         }      SHFT(*ax,*bx,*cx,u) 
         if (ij > ncodemax[j]) break;      SHFT(*fa,*fb,*fc,fu) 
       }    #ifdef DEBUG
     }        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);
   #endif
  for (k=0; k<19; k++) Ndum[k]=0;    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
   } 
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];  /*************** linmin ************************/
       Ndum[ij]++;  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
     }  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   and replaces xi by the actual vector displacement that p was moved. Also returns as fret
  ij=1;  the value of func at the returned location p . This is actually all accomplished by calling the
  for (i=1; i<=10; i++) {  routines mnbrak and brent .*/
    if((Ndum[i]!=0) && (i<=ncovcol)){  int ncom; 
      Tvaraff[ij]=i;  double *pcom,*xicom;
      ij++;  double (*nrfunc)(double []); 
    }   
  }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
    { 
     cptcoveff=ij-1;    double brent(double ax, double bx, double cx, 
 }                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 /*********** Health Expectancies ****************/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)    int j; 
 {    double xx,xmin,bx,ax; 
   /* Health expectancies */    double fx,fb,fa;
   int i, j, nhstepm, hstepm, h, nstepm;  
   double age, agelim, hf;    double scale=10., axs, xxs, xxss; /* Scale added for infinity */
   double ***p3mat;   
      ncom=n; 
   fprintf(ficreseij,"# Health expectancies\n");    pcom=vector(1,n); 
   fprintf(ficreseij,"# Age");    xicom=vector(1,n); 
   for(i=1; i<=nlstate;i++)    nrfunc=func; 
     for(j=1; j<=nlstate;j++)    for (j=1;j<=n;j++) { 
       fprintf(ficreseij," %1d-%1d",i,j);      pcom[j]=p[j]; 
   fprintf(ficreseij,"\n");      xicom[j]=xi[j]; 
     } 
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);    axs=0.0;
   }    xxss=1; /* 1 and using scale */
   else  hstepm=estepm;      xxs=1;
   /* We compute the life expectancy from trapezoids spaced every estepm months    do{
    * This is mainly to measure the difference between two models: for example      ax=0.;
    * if stepm=24 months pijx are given only every 2 years and by summing them      xx= xxs;
    * we are calculating an estimate of the Life Expectancy assuming a linear      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
    * progression inbetween and thus overestimating or underestimating according      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
    * to the curvature of the survival function. If, for the same date, we      /* 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))   */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
    * to compare the new estimate of Life expectancy with the same linear      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
    * hypothesis. A more precise result, taking into account a more precise      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
    * curvature will be obtained if estepm is as small as stepm. */      /* 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]]*/
       if (fx != fx){
   /* For example we decided to compute the life expectancy with the smallest unit */          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          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);
      nhstepm is the number of hstepm from age to agelim      }
      nstepm is the number of stepm from age to agelin.    }while(fx != fx);
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like estepm months */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
      survival function given by stepm (the optimization length). Unfortunately it    /* fmin = f(p[j] + xmin * xi[j]) */
      means that if the survival funtion is printed only each two years of age and if    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
      results. So we changed our mind and took the option of the best precision.  #ifdef DEBUG
   */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
   agelim=AGESUP;    /* printf("linmin end "); */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (j=1;j<=n;j++) { 
     /* nhstepm age range expressed in number of stepm */      /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      /* if(xxs <1.0) */
     /* if (stepm >= YEARM) hstepm=1;*/      /*   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 ); */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      p[j] += xi[j]; /* Parameters values are updated accordingly */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    /* printf("\n"); */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    /* printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", *fret, (*func)(p)); */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      free_vector(xicom,1,n); 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    free_vector(pcom,1,n); 
     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] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  /*************** powell ************************/
           /* 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]);*/  /*
         }  Minimization of a function func of n variables. Input consists of an initial starting point
     fprintf(ficreseij,"%3.0f",age );  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
     for(i=1; i<=nlstate;i++)  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
       for(j=1; j<=nlstate;j++){  such that failure to decrease by more than this amount on one iteration signals doneness. On
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
       }  function value at p , and iter is the number of iterations taken. The routine linmin is used.
     fprintf(ficreseij,"\n");   */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   }              double (*func)(double [])) 
 }  { 
     void linmin(double p[], double xi[], int n, double *fret, 
 /************ Variance ******************/                double (*func)(double [])); 
 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)    int i,ibig,j; 
 {    double del,t,*pt,*ptt,*xit;
   /* Variance of health expectancies */    double directest;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double fp,fptt;
   double **newm;    double *xits;
   double **dnewm,**doldm;    int niterf, itmp;
   int i, j, nhstepm, hstepm, h, nstepm ;  
   int k, cptcode;    pt=vector(1,n); 
   double *xp;    ptt=vector(1,n); 
   double **gp, **gm;    xit=vector(1,n); 
   double ***gradg, ***trgradg;    xits=vector(1,n); 
   double ***p3mat;    *fret=(*func)(p); 
   double age,agelim, hf;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   int theta;      rcurr_time = time(NULL);  
     for (*iter=1;;++(*iter)) { 
    fprintf(ficresvij,"# Covariances of life expectancies\n");      fp=(*fret); /* From former iteration or initial value */
   fprintf(ficresvij,"# Age");      ibig=0; 
   for(i=1; i<=nlstate;i++)      del=0.0; 
     for(j=1; j<=nlstate;j++)      rlast_time=rcurr_time;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      /* (void) gettimeofday(&curr_time,&tzp); */
   fprintf(ficresvij,"\n");      rcurr_time = time(NULL);  
       curr_time = *localtime(&rcurr_time);
   xp=vector(1,npar);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
   dnewm=matrix(1,nlstate,1,npar);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   doldm=matrix(1,nlstate,1,nlstate);  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
       for (i=1;i<=n;i++) {
   if(estepm < stepm){        printf(" %d %.12f",i, p[i]);
     printf ("Problem %d lower than %d\n",estepm, stepm);        fprintf(ficlog," %d %.12lf",i, p[i]);
   }        fprintf(ficrespow," %.12lf", p[i]);
   else  hstepm=estepm;        }
   /* For example we decided to compute the life expectancy with the smallest unit */      printf("\n");
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      fprintf(ficlog,"\n");
      nhstepm is the number of hstepm from age to agelim      fprintf(ficrespow,"\n");fflush(ficrespow);
      nstepm is the number of stepm from age to agelin.      if(*iter <=3){
      Look at hpijx to understand the reason of that which relies in memory size        tml = *localtime(&rcurr_time);
      and note for a fixed period like k years */        strcpy(strcurr,asctime(&tml));
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        rforecast_time=rcurr_time; 
      survival function given by stepm (the optimization length). Unfortunately it        itmp = strlen(strcurr);
      means that if the survival funtion is printed only each two years of age and if        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          strcurr[itmp-1]='\0';
      results. So we changed our mind and took the option of the best precision.        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);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        for(niterf=10;niterf<=30;niterf+=10){
   agelim = AGESUP;          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          forecast_time = *localtime(&rforecast_time);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          strcpy(strfor,asctime(&forecast_time));
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          itmp = strlen(strfor);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if(strfor[itmp-1]=='\n')
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          strfor[itmp-1]='\0';
     gp=matrix(0,nhstepm,1,nlstate);          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);
     gm=matrix(0,nhstepm,1,nlstate);          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);
         }
     for(theta=1; theta <=npar; theta++){      }
       for(i=1; i<=npar; i++){ /* Computes gradient */      for (i=1;i<=n;i++) { /* For each direction i */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
       }        fptt=(*fret); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #ifdef DEBUG
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
             fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       if (popbased==1) {  #endif
         for(i=1; i<=nlstate;i++)            printf("%d",i);fflush(stdout); /* print direction (parameter) i */
           prlim[i][i]=probs[(int)age][i][ij];        fprintf(ficlog,"%d",i);fflush(ficlog);
       }        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                                        /* Outputs are fret(new point p) p is updated and xit rescaled */
       for(j=1; j<= nlstate; j++){        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
         for(h=0; h<=nhstepm; h++){          /* because that direction will be replaced unless the gain del is small */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
         }          /* with the new direction. */
       }          del=fabs(fptt-(*fret)); 
              ibig=i; 
       for(i=1; i<=npar; i++) /* Computes gradient */        } 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  #ifdef DEBUG
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          printf("%d %.12e",i,(*fret));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        fprintf(ficlog,"%d %.12e",i,(*fret));
          for (j=1;j<=n;j++) {
       if (popbased==1) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         for(i=1; i<=nlstate;i++)          printf(" x(%d)=%.12e",j,xit[j]);
           prlim[i][i]=probs[(int)age][i][ij];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
         for(j=1;j<=n;j++) {
       for(j=1; j<= nlstate; j++){          printf(" p(%d)=%.12e",j,p[j]);
         for(h=0; h<=nhstepm; h++){          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        printf("\n");
         }        fprintf(ficlog,"\n");
       }  #endif
       } /* end loop on each direction i */
       for(j=1; j<= nlstate; j++)      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
         for(h=0; h<=nhstepm; h++){      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      /* New value of last point Pn is not computed, P(n-1) */
         }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
     } /* End theta */        /* 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 */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
         /* decreased of more than 3.84  */
     for(h=0; h<=nhstepm; h++)        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
       for(j=1; j<=nlstate;j++)        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
         for(theta=1; theta <=npar; theta++)        /* By adding 10 parameters more the gain should be 18.31 */
           trgradg[h][j][theta]=gradg[h][theta][j];  
         /* Starting the program with initial values given by a former maximization will simply change */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        /* the scales of the directions and the directions, because the are reset to canonical directions */
     for(i=1;i<=nlstate;i++)        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
       for(j=1;j<=nlstate;j++)        /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
         vareij[i][j][(int)age] =0.;  #ifdef DEBUG
         int k[2],l;
     for(h=0;h<=nhstepm;h++){        k[0]=1;
       for(k=0;k<=nhstepm;k++){        k[1]=-1;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        printf("Max: %.12e",(*func)(p));
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for(i=1;i<=nlstate;i++)        for (j=1;j<=n;j++) {
           for(j=1;j<=nlstate;j++)          printf(" %.12e",p[j]);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          fprintf(ficlog," %.12e",p[j]);
       }        }
     }        printf("\n");
         fprintf(ficlog,"\n");
     fprintf(ficresvij,"%.0f ",age );        for(l=0;l<=1;l++) {
     for(i=1; i<=nlstate;i++)          for (j=1;j<=n;j++) {
       for(j=1; j<=nlstate;j++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     fprintf(ficresvij,"\n");          }
     free_matrix(gp,0,nhstepm,1,nlstate);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     free_matrix(gm,0,nhstepm,1,nlstate);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  #endif
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */  
          free_vector(xit,1,n); 
   free_vector(xp,1,npar);        free_vector(xits,1,n); 
   free_matrix(doldm,1,nlstate,1,npar);        free_vector(ptt,1,n); 
   free_matrix(dnewm,1,nlstate,1,nlstate);        free_vector(pt,1,n); 
         return; 
 }      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 /************ Variance of prevlim ******************/      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
 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)        ptt[j]=2.0*p[j]-pt[j]; 
 {        xit[j]=p[j]-pt[j]; 
   /* Variance of prevalence limit */        pt[j]=p[j]; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      } 
   double **newm;      fptt=(*func)(ptt); /* f_3 */
   double **dnewm,**doldm;      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   int i, j, nhstepm, hstepm;        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
   int k, cptcode;        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
   double *xp;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
   double *gp, *gm;        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   double **gradg, **trgradg;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
   double age,agelim;        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
   int theta;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
      #ifdef NRCORIGINAL
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   fprintf(ficresvpl,"# Age");  #else
   for(i=1; i<=nlstate;i++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       fprintf(ficresvpl," %1d-%1d",i,i);        t= t- del*SQR(fp-fptt);
   fprintf(ficresvpl,"\n");  #endif
         directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
   xp=vector(1,npar);  #ifdef DEBUG
   dnewm=matrix(1,nlstate,1,npar);        printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
   doldm=matrix(1,nlstate,1,nlstate);        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
          printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   hstepm=1*YEARM; /* Every year of age */               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   agelim = AGESUP;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        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);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        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);
     if (stepm >= YEARM) hstepm=1;  #endif
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  #ifdef POWELLORIGINAL
     gradg=matrix(1,npar,1,nlstate);        if (t < 0.0) { /* Then we use it for new direction */
     gp=vector(1,nlstate);  #else
     gm=vector(1,nlstate);        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(theta=1; theta <=npar; theta++){        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       for(i=1; i<=npar; i++){ /* Computes gradient */        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       }      } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if (directest < 0.0) { /* Then we use it for new direction */
       for(i=1;i<=nlstate;i++)  #endif
         gp[i] = prlim[i][i];          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
              for (j=1;j<=n;j++) { 
       for(i=1; i<=npar; i++) /* Computes gradient */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
       for(i=1;i<=nlstate;i++)          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
         gm[i] = prlim[i][i];          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   
       for(i=1;i<=nlstate;i++)  #ifdef DEBUG
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     } /* End theta */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
     trgradg =matrix(1,nlstate,1,npar);            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
     for(j=1; j<=nlstate;j++)          }
       for(theta=1; theta <=npar; theta++)          printf("\n");
         trgradg[j][theta]=gradg[theta][j];          fprintf(ficlog,"\n");
   #endif
     for(i=1;i<=nlstate;i++)        } /* end of t negative */
       varpl[i][(int)age] =0.;      } /* end if (fptt < fp)  */
     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 */  /**** Prevalence limit (stable or period prevalence)  ****************/
   
     fprintf(ficresvpl,"%.0f ",age );  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(i=1; i<=nlstate;i++)  {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     fprintf(ficresvpl,"\n");       matrix by transitions matrix until convergence is reached */
     free_vector(gp,1,nlstate);    
     free_vector(gm,1,nlstate);    int i, ii,j,k;
     free_matrix(gradg,1,npar,1,nlstate);    double min, max, maxmin, maxmax,sumnew=0.;
     free_matrix(trgradg,1,nlstate,1,npar);    /* double **matprod2(); */ /* test */
   } /* End age */    double **out, cov[NCOVMAX+1], **pmij();
     double **newm;
   free_vector(xp,1,npar);    double agefin, delaymax=50 ; /* Max number of years to converge */
   free_matrix(doldm,1,nlstate,1,npar);    
   free_matrix(dnewm,1,nlstate,1,nlstate);    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
 }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
 /************ Variance of one-step probabilities  ******************/    
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    cov[1]=1.;
 {    
   int i, j;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int k=0, cptcode;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double **dnewm,**doldm;      newm=savm;
   double *xp;      /* Covariates have to be included here again */
   double *gp, *gm;      cov[2]=agefin;
   double **gradg, **trgradg;      if(nagesqr==1)
   double age,agelim, cov[NCOVMAX];        cov[3]= agefin*agefin;;
   int theta;      for (k=1; k<=cptcovn;k++) {
   char fileresprob[FILENAMELENGTH];        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
   strcpy(fileresprob,"prob");      }
   strcat(fileresprob,fileres);      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
     printf("Problem with resultfile: %s\n", fileresprob);      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]]];
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      
        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   xp=vector(1,npar);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
        out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   cov[1]=1;      
   for (age=bage; age<=fage; age ++){      savm=oldm;
     cov[2]=age;      oldm=newm;
     gradg=matrix(1,npar,1,9);      maxmax=0.;
     trgradg=matrix(1,9,1,npar);      for(j=1;j<=nlstate;j++){
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        min=1.;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        max=0.;
            for(i=1; i<=nlstate; i++) {
     for(theta=1; theta <=npar; theta++){          sumnew=0;
       for(i=1; i<=npar; i++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          prlim[i][j]= newm[i][j]/(1-sumnew);
                /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          max=FMAX(max,prlim[i][j]);
              min=FMIN(min,prlim[i][j]);
       k=0;        }
       for(i=1; i<= (nlstate+ndeath); i++){        maxmin=max-min;
         for(j=1; j<=(nlstate+ndeath);j++){        maxmax=FMAX(maxmax,maxmin);
            k=k+1;      } /* j loop */
           gp[k]=pmmij[i][j];      if(maxmax < ftolpl){
         }        return prlim;
       }      }
     } /* age loop */
       for(i=1; i<=npar; i++)    return prlim; /* should not reach here */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  }
      
   /*************** transition probabilities ***************/ 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
       k=0;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for(i=1; i<=(nlstate+ndeath); i++){  {
         for(j=1; j<=(nlstate+ndeath);j++){    /* According to parameters values stored in x and the covariate's values stored in cov,
           k=k+1;       computes the probability to be observed in state j being in state i by appying the
           gm[k]=pmmij[i][j];       model to the ncovmodel covariates (including constant and age).
         }       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
       }       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
             ncth covariate in the global vector x is given by the formula:
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];         j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     }       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)       Outputs ps[i][j] the probability to be observed in j being in j according to
       for(theta=1; theta <=npar; theta++)       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
       trgradg[j][theta]=gradg[theta][j];    */
      double s1, lnpijopii;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    /*double t34;*/
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    int i,j, nc, ii, jj;
   
      pmij(pmmij,cov,ncovmodel,x,nlstate);      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
      k=0;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
      for(i=1; i<=(nlstate+ndeath); i++){            /*lnpijopii += param[i][j][nc]*cov[nc];*/
        for(j=1; j<=(nlstate+ndeath);j++){            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
          k=k+1;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
          gm[k]=pmmij[i][j];          }
         }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
      }  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
              }
      /*printf("\n%d ",(int)age);        for(j=i+1; j<=nlstate+ndeath;j++){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                    /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
             lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
      }*/          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   fprintf(ficresprob,"\n%d ",(int)age);        }
       }
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      for(i=1; i<= nlstate; i++){
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        s1=0;
   }        for(j=1; j<i; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(j=i+1; j<=nlstate+ndeath; j++){
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          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); */
  free_vector(xp,1,npar);        }
 fclose(ficresprob);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         ps[i][i]=1./(s1+1.);
 }        /* Computing other pijs */
         for(j=1; j<i; j++)
 /******************* Printing html file ***********/          ps[i][j]= exp(ps[i][j])*ps[i][i];
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        for(j=i+1; j<=nlstate+ndeath; j++)
  int lastpass, int stepm, int weightopt, char model[],\          ps[i][j]= exp(ps[i][j])*ps[i][i];
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      } /* end i */
  char version[], int popforecast, int estepm ){      
   int jj1, k1, i1, cpt;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   FILE *fichtm;        for(jj=1; jj<= nlstate+ndeath; jj++){
   /*char optionfilehtm[FILENAMELENGTH];*/          ps[ii][jj]=0;
           ps[ii][ii]=1;
   strcpy(optionfilehtm,optionfile);        }
   strcat(optionfilehtm,".htm");      }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      
     printf("Problem with %s \n",optionfilehtm), exit(0);      
   }      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      /*   } */
 \n      /*   printf("\n "); */
 Total number of observations=%d <br>\n      /* } */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      /* printf("\n ");printf("%lf ",cov[2]);*/
 <hr  size=\"2\" color=\"#EC5E5E\">      /*
  <ul><li>Outputs files<br>\n        for(i=1; i<= npar; i++) printf("%f ",x[i]);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        goto end;*/
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n      return ps;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  }
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n  
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n  /**************** Product of 2 matrices ******************/
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);  
   double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
  fprintf(fichtm,"\n  {
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    /* in, b, out are matrice of pointers which should have been initialized 
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
  if(popforecast==1) fprintf(fichtm,"\n    int i, j, k;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    for(i=nrl; i<= nrh; i++)
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      for(k=ncolol; k<=ncoloh; k++){
         <br>",fileres,fileres,fileres,fileres);        out[i][k]=0.;
  else        for(j=ncl; j<=nch; j++)
    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);          out[i][k] +=in[i][j]*b[j][k];
 fprintf(fichtm," <li>Graphs</li><p>");      }
     return out;
  m=cptcoveff;  }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   
  jj1=0;  /************* Higher Matrix Product ***************/
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
        jj1++;  {
        if (cptcovn > 0) {    /* Computes the transition matrix starting at age 'age' over 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");       'nhstepm*hstepm*stepm' months (i.e. until
          for (cpt=1; cpt<=cptcoveff;cpt++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);       nhstepm*hstepm matrices. 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");       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(fichtm,"<br>- Probabilities: pe%s%d.gif<br>       for the memory).
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);           Model is determined by parameters x and covariates have to be 
        for(cpt=1; cpt<nlstate;cpt++){       included manually here. 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       */
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {    int i, j, d, h, k;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    double **out, cov[NCOVMAX+1];
 interval) in state (%d): v%s%d%d.gif <br>    double **newm;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      double agexact;
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {    /* Hstepm could be zero and should return the unit matrix */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    for (i=1;i<=nlstate+ndeath;i++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for (j=1;j<=nlstate+ndeath;j++){
      }        oldm[i][j]=(i==j ? 1.0 : 0.0);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        po[i][j][0]=(i==j ? 1.0 : 0.0);
 health expectancies in states (1) and (2): e%s%d.gif<br>      }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 fprintf(fichtm,"\n</body>");    for(h=1; h <=nhstepm; h++){
    }      for(d=1; d <=hstepm; d++){
    }        newm=savm;
 fclose(fichtm);        /* Covariates have to be included here again */
 }        cov[1]=1.;
         agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 /******************* Gnuplot file **************/        cov[2]=agexact;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        if(nagesqr==1)
           cov[3]= agexact*agexact;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        for (k=1; k<=cptcovn;k++) 
           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   strcpy(optionfilegnuplot,optionfilefiname);        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
   strcat(optionfilegnuplot,".gp.txt");          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
     printf("Problem with file %s",optionfilegnuplot);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   }          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 #endif        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 m=pow(2,cptcoveff);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                       pmij(pmmij,cov,ncovmodel,x,nlstate));
  /* 1eme*/        savm=oldm;
   for (cpt=1; cpt<= nlstate ; cpt ++) {        oldm=newm;
    for (k1=1; k1<= m ; k1 ++) {      }
       for(i=1; i<=nlstate+ndeath; i++)
 #ifdef windows        for(j=1;j<=nlstate+ndeath;j++) {
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          po[i][j][h]=newm[i][j];
 #endif          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
 #ifdef unix        }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      /*printf("h=%d ",h);*/
 #endif    } /* end h */
   /*     printf("\n H=%d \n",h); */
 for (i=1; i<= nlstate ; i ++) {    return po;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  #ifdef NLOPT
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     for (i=1; i<= nlstate ; i ++) {    double fret;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double *xt;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int j;
 }    myfunc_data *d2 = (myfunc_data *) pd;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  /* xt = (p1-1); */
      for (i=1; i<= nlstate ; i ++) {    xt=vector(1,n); 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
 #ifdef unix    printf("Function = %.12lf ",fret);
 fprintf(ficgp,"\nset ter gif small size 400,300");    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
 #endif    printf("\n");
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);   free_vector(xt,1,n);
    }    return fret;
   }  }
   /*2 eme*/  #endif
   
   for (k1=1; k1<= m ; k1 ++) {  /*************** log-likelihood *************/
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);  double func( double *x)
      {
     for (i=1; i<= nlstate+1 ; i ++) {    int i, ii, j, k, mi, d, kk;
       k=2*i;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    double **out;
       for (j=1; j<= nlstate+1 ; j ++) {    double sw; /* Sum of weights */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double lli; /* Individual log likelihood */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int s1, s2;
 }      double bbh, survp;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    long ipmx;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double agexact;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*extern weight */
       for (j=1; j<= nlstate+1 ; j ++) {    /* We are differentiating ll according to initial status */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");    /*for(i=1;i<imx;i++) 
 }        printf(" %d\n",s[4][i]);
       fprintf(ficgp,"\" t\"\" w l 0,");    */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    ++countcallfunc;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    cov[1]=1.;
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    for(k=1; k<=nlstate; k++) ll[k]=0.;
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }    if(mle==1){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        /* Computes the values of the ncovmodel covariates of the model
             depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   /*3eme*/           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
            to be observed in j being in i according to the model.
   for (k1=1; k1<= m ; k1 ++) {         */
     for (cpt=1; cpt<= nlstate ; cpt ++) {        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
       k=2+nlstate*(cpt-1);            cov[2+nagesqr+k]=covar[Tvar[k]][i];
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        }
       for (i=1; i< nlstate ; i ++) {        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       }           has been calculated etc */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* CV preval stat */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (k1=1; k1<= m ; k1 ++) {            }
     for (cpt=1; cpt<nlstate ; cpt ++) {          for(d=0; d<dh[mi][i]; d++){
       k=3;            newm=savm;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
       for (i=1; i< nlstate ; i ++)            if(nagesqr==1)
         fprintf(ficgp,"+$%d",k+i+1);              cov[3]= agexact*agexact;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
       l=3+(nlstate+ndeath)*cpt;            }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (i=1; i< nlstate ; i ++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         l=3+(nlstate+ndeath)*cpt;            savm=oldm;
         fprintf(ficgp,"+$%d",l+i+1);            oldm=newm;
       }          } /* end mult */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     }          /* But now since version 0.9 we anticipate for bias at large stepm.
   }             * If stepm is larger than one month (smallest stepm) and if the exact delay 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
   /* proba elementaires */           * the nearest (and in case of equal distance, to the lowest) interval but now
    for(i=1,jk=1; i <=nlstate; i++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for(k=1; k <=(nlstate+ndeath); k++){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       if (k != i) {           * probability in order to take into account the bias as a fraction of the way
         for(j=1; j <=ncovmodel; j++){           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                   * -stepm/2 to stepm/2 .
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);           * For stepm=1 the results are the same as for previous versions of Imach.
           jk++;           * For stepm > 1 the results are less biased than in previous versions. 
           fprintf(ficgp,"\n");           */
         }          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
     }          bbh=(double)bh[mi][i]/(double)stepm; 
     }          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
     for(jk=1; jk <=m; jk++) {           */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
    i=1;          if( s2 > nlstate){ 
    for(k2=1; k2<=nlstate; k2++) {            /* i.e. if s2 is a death state and if the date of death is known 
      k3=i;               then the contribution to the likelihood is the probability to 
      for(k=1; k<=(nlstate+ndeath); k++) {               die between last step unit time and current  step unit time, 
        if (k != k2){               which is also equal to probability to die before dh 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);               minus probability to die before dh-stepm . 
 ij=1;               In version up to 0.92 likelihood was computed
         for(j=3; j <=ncovmodel; j++) {          as if date of death was unknown. Death was treated as any other
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          health state: the date of the interview describes the actual state
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          and not the date of a change in health state. The former idea was
             ij++;          to consider that at each interview the state was recorded
           }          (healthy, disable or death) and IMaCh was corrected; but when we
           else          introduced the exact date of death then we should have modified
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          the contribution of an exact death to the likelihood. This new
         }          contribution is smaller and very dependent of the step unit
           fprintf(ficgp,")/(1");          stepm. It is no more the probability to die between last interview
                  and month of death but the probability to survive from last
         for(k1=1; k1 <=nlstate; k1++){            interview up to one month before death multiplied by the
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          probability to die within a month. Thanks to Chris
 ij=1;          Jackson for correcting this bug.  Former versions increased
           for(j=3; j <=ncovmodel; j++){          mortality artificially. The bad side is that we add another loop
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          which slows down the processing. The difference can be up to 10%
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          lower mortality.
             ij++;            */
           }          /* If, at the beginning of the maximization mostly, the
           else             cumulative probability or probability to be dead is
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);             constant (ie = 1) over time d, the difference is equal to
           }             0.  out[s1][3] = savm[s1][3]: probability, being at state
           fprintf(ficgp,")");             s1 at precedent wave, to be dead a month before current
         }             wave is equal to probability, being at state s1 at
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);             precedent wave, to be dead at mont of the current
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");             wave. Then the observed probability (that this person died)
         i=i+ncovmodel;             is null according to current estimated parameter. In fact,
        }             it should be very low but not zero otherwise the log go to
      }             infinity.
    }          */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  /* #ifdef INFINITYORIGINAL */
    }  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
      /* #else */
   fclose(ficgp);  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
 }  /* end gnuplot */  /*          lli=log(mytinydouble); */
   /*        else */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /*************** Moving average **************/  /* #endif */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              lli=log(out[s1][s2] - savm[s1][s2]);
   
   int i, cpt, cptcod;          } else if  (s2==-2) {
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)            for (j=1,survp=0. ; j<=nlstate; j++) 
       for (i=1; i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            /*survp += out[s1][j]; */
           mobaverage[(int)agedeb][i][cptcod]=0.;            lli= log(survp);
              }
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          
       for (i=1; i<=nlstate;i++){          else if  (s2==-4) { 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for (j=3,survp=0. ; j<=nlstate; j++)  
           for (cpt=0;cpt<=4;cpt++){              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            lli= log(survp); 
           }          } 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }          else if  (s2==-5) { 
       }            for (j=1,survp=0. ; j<=2; j++)  
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                lli= log(survp); 
 }          } 
           
           else{
 /************** Forecasting ******************/            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 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){            /*  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 */
            } 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int *popage;          /*if(lli ==000.0)*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          /*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); */
   double *popeffectif,*popcount;          ipmx +=1;
   double ***p3mat;          sw += weight[i];
   char fileresf[FILENAMELENGTH];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /* if (lli < log(mytinydouble)){ */
  agelim=AGESUP;          /*   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); */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          /*   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]); */
           /* } */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        } /* end of wave */
        } /* end of individual */
      }  else if(mle==2){
   strcpy(fileresf,"f");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcat(fileresf,fileres);        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   if((ficresf=fopen(fileresf,"w"))==NULL) {        for(mi=1; mi<= wav[i]-1; mi++){
     printf("Problem with forecast resultfile: %s\n", fileresf);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   printf("Computing forecasting: result on file '%s' \n", fileresf);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            }
           for(d=0; d<=dh[mi][i]; d++){
   if (mobilav==1) {            newm=savm;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
     movingaverage(agedeb, fage, ageminpar, mobaverage);            cov[2]=agexact;
   }            if(nagesqr==1)
               cov[3]= agexact*agexact;
   stepsize=(int) (stepm+YEARM-1)/YEARM;            for (kk=1; kk<=cptcovage;kk++) {
   if (stepm<=12) stepsize=1;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
              }
   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);          bbh=(double)bh[mi][i]/(double)stepm; 
   jprojmean=yp;          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 */
   if(jprojmean==0) jprojmean=1;          ipmx +=1;
   if(mprojmean==0) jprojmean=1;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   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++){    }  else if(mle==3){  /* exponential inter-extrapolation */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       k=k+1;        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       fprintf(ficresf,"\n#******");        for(mi=1; mi<= wav[i]-1; mi++){
       for(j=1;j<=cptcoveff;j++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresf,"******\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresf,"# StartingAge FinalAge");            }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          for(d=0; d<dh[mi][i]; d++){
                  newm=savm;
                  agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            cov[2]=agexact;
         fprintf(ficresf,"\n");            if(nagesqr==1)
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            }
           nhstepm = nhstepm/hstepm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                   1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            savm=oldm;
           oldm=oldms;savm=savms;            oldm=newm;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            } /* end mult */
                
           for (h=0; h<=nhstepm; h++){          s1=s[mw[mi][i]][i];
             if (h==(int) (calagedate+YEARM*cpt)) {          s2=s[mw[mi+1][i]][i];
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          bbh=(double)bh[mi][i]/(double)stepm; 
             }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
             for(j=1; j<=nlstate+ndeath;j++) {          ipmx +=1;
               kk1=0.;kk2=0;          sw += weight[i];
               for(i=1; i<=nlstate;i++) {                        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                 if (mobilav==1)        } /* end of wave */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      } /* end of individual */
                 else {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                 }        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                        for(mi=1; mi<= wav[i]-1; mi++){
               }          for (ii=1;ii<=nlstate+ndeath;ii++)
               if (h==(int)(calagedate+12*cpt)){            for (j=1;j<=nlstate+ndeath;j++){
                 fprintf(ficresf," %.3f", kk1);              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++){
           }            newm=savm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            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++) {
                      cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
           
   fclose(ficresf);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /************** Forecasting ******************/            savm=oldm;
 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){            oldm=newm;
            } /* end mult */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        
   int *popage;          s1=s[mw[mi][i]][i];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          s2=s[mw[mi+1][i]][i];
   double *popeffectif,*popcount;          if( s2 > nlstate){ 
   double ***p3mat,***tabpop,***tabpopprev;            lli=log(out[s1][s2] - savm[s1][s2]);
   char filerespop[FILENAMELENGTH];          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          ipmx +=1;
   agelim=AGESUP;          sw += weight[i];
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          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]); */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        } /* end of wave */
        } /* end of individual */
      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   strcpy(filerespop,"pop");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcat(filerespop,fileres);        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        for(mi=1; mi<= wav[i]-1; mi++){
     printf("Problem with forecast resultfile: %s\n", filerespop);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   printf("Computing forecasting: result on file '%s' \n", filerespop);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            }
           for(d=0; d<dh[mi][i]; d++){
   if (mobilav==1) {            newm=savm;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
     movingaverage(agedeb, fage, ageminpar, mobaverage);            cov[2]=agexact;
   }            if(nagesqr==1)
               cov[3]= agexact*agexact;
   stepsize=(int) (stepm+YEARM-1)/YEARM;            for (kk=1; kk<=cptcovage;kk++) {
   if (stepm<=12) stepsize=1;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
              }
   agelim=AGESUP;          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   hstepm=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   hstepm=hstepm/stepm;            savm=oldm;
              oldm=newm;
   if (popforecast==1) {          } /* end mult */
     if((ficpop=fopen(popfile,"r"))==NULL) {        
       printf("Problem with population file : %s\n",popfile);exit(0);          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
     popage=ivector(0,AGESUP);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     popeffectif=vector(0,AGESUP);          ipmx +=1;
     popcount=vector(0,AGESUP);          sw += weight[i];
              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     i=1;            /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        } /* end of wave */
          } /* end of individual */
     imx=i;    } /* End of if */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   for(cptcov=1;cptcov<=i2;cptcov++){    return -l;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  }
       k=k+1;  
       fprintf(ficrespop,"\n#******");  /*************** log-likelihood *************/
       for(j=1;j<=cptcoveff;j++) {  double funcone( double *x)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  {
       }    /* Same as likeli but slower because of a lot of printf and if */
       fprintf(ficrespop,"******\n");    int i, ii, j, k, mi, d, kk;
       fprintf(ficrespop,"# Age");    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    double **out;
       if (popforecast==1)  fprintf(ficrespop," [Population]");    double lli; /* Individual log likelihood */
          double llt;
       for (cpt=0; cpt<=0;cpt++) {    int s1, s2;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      double bbh, survp;
            double agexact;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    /*extern weight */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /* We are differentiating ll according to initial status */
           nhstepm = nhstepm/hstepm;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
              /*for(i=1;i<imx;i++) 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf(" %d\n",s[4][i]);
           oldm=oldms;savm=savms;    */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      cov[1]=1.;
          
           for (h=0; h<=nhstepm; h++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             }      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
             for(j=1; j<=nlstate+ndeath;j++) {      for(mi=1; mi<= wav[i]-1; mi++){
               kk1=0.;kk2=0;        for (ii=1;ii<=nlstate+ndeath;ii++)
               for(i=1; i<=nlstate;i++) {                        for (j=1;j<=nlstate+ndeath;j++){
                 if (mobilav==1)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                 else {          }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        for(d=0; d<dh[mi][i]; d++){
                 }          newm=savm;
               }          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
               if (h==(int)(calagedate+12*cpt)){          cov[2]=agexact;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          if(nagesqr==1)
                   /*fprintf(ficrespop," %.3f", kk1);            cov[3]= agexact*agexact;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          for (kk=1; kk<=cptcovage;kk++) {
               }            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             }          }
             for(i=1; i<=nlstate;i++){  
               kk1=0.;          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                 for(j=1; j<=nlstate;j++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                 }          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
             }          savm=oldm;
           oldm=newm;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        } /* end mult */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        
           }        s1=s[mw[mi][i]][i];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        s2=s[mw[mi+1][i]][i];
         }        bbh=(double)bh[mi][i]/(double)stepm; 
       }        /* bias is positive if real duration
           * is higher than the multiple of stepm and negative otherwise.
   /******/         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          lli=log(out[s1][s2] - savm[s1][s2]);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          } else if  (s2==-2) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for (j=1,survp=0. ; j<=nlstate; j++) 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           nhstepm = nhstepm/hstepm;          lli= log(survp);
                  }else if (mle==1){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           oldm=oldms;savm=savms;        } else if(mle==2){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           for (h=0; h<=nhstepm; h++){        } else if(mle==3){  /* exponential inter-extrapolation */
             if (h==(int) (calagedate+YEARM*cpt)) {          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 */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
             }          lli=log(out[s1][s2]); /* Original formula */
             for(j=1; j<=nlstate+ndeath;j++) {        } else{  /* mle=0 back to 1 */
               kk1=0.;kk2=0;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
               for(i=1; i<=nlstate;i++) {                        /*lli=log(out[s1][s2]); */ /* Original formula */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            } /* End of if */
               }        ipmx +=1;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        sw += weight[i];
             }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           }        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if(globpr){
         }          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       }   %11.6f %11.6f %11.6f ", \
    }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   if (popforecast==1) {          }
     free_ivector(popage,0,AGESUP);          fprintf(ficresilk," %10.6f\n", -llt);
     free_vector(popeffectif,0,AGESUP);        }
     free_vector(popcount,0,AGESUP);      } /* end of wave */
   }    } /* end of individual */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   fclose(ficrespop);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 }    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
 /***********************************************/      gsw=sw;
 /**************** Main Program *****************/    }
 /***********************************************/    return -l;
   }
 int main(int argc, char *argv[])  
 {  
   /*************** function likelione ***********/
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   double agedeb, agefin,hf;  {
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
   double fret;       to check the exact contribution to the likelihood.
   double **xi,tmp,delta;       Plotting could be done.
      */
   double dum; /* Dummy variable */    int k;
   double ***p3mat;  
   int *indx;    if(*globpri !=0){ /* Just counts and sums, no printings */
   char line[MAXLINE], linepar[MAXLINE];      strcpy(fileresilk,"ilk"); 
   char title[MAXLINE];      strcat(fileresilk,fileres);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        printf("Problem with resultfile: %s\n", fileresilk);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      }
       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");
   char filerest[FILENAMELENGTH];      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   char fileregp[FILENAMELENGTH];      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   char popfile[FILENAMELENGTH];      for(k=1; k<=nlstate; k++) 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   int firstobs=1, lastobs=10;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   int sdeb, sfin; /* Status at beginning and end */    }
   int c,  h , cpt,l;  
   int ju,jl, mi;    *fretone=(*funcone)(p);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    if(*globpri !=0){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      fclose(ficresilk);
   int mobilav=0,popforecast=0;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   int hstepm, nhstepm;      fflush(fichtm); 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    } 
     return;
   double bage, fage, age, agelim, agebase;  }
   double ftolpl=FTOL;  
   double **prlim;  
   double *severity;  /*********** Maximum Likelihood Estimation ***************/
   double ***param; /* Matrix of parameters */  
   double  *p;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double **matcov; /* Matrix of covariance */  {
   double ***delti3; /* Scale */    int i,j, iter=0;
   double *delti; /* Scale */    double **xi;
   double ***eij, ***vareij;    double fret;
   double **varpl; /* Variances of prevalence limits by age */    double fretone; /* Only one call to likelihood */
   double *epj, vepp;    /*  char filerespow[FILENAMELENGTH];*/
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  #ifdef NLOPT
      int creturn;
     nlopt_opt opt;
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double *lb;
     double minf; /* the minimum objective value, upon return */
     double * p1; /* Shifted parameters from 0 instead of 1 */
   char z[1]="c", occ;    myfunc_data dinst, *d = &dinst;
 #include <sys/time.h>  #endif
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
      xi=matrix(1,npar,1,npar);
   /* long total_usecs;    for (i=1;i<=npar;i++)
   struct timeval start_time, end_time;      for (j=1;j<=npar;j++)
          xi[i][j]=(i==j ? 1.0 : 0.0);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   getcwd(pathcd, size);    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
   printf("\n%s",version);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   if(argc <=1){      printf("Problem with resultfile: %s\n", filerespow);
     printf("\nEnter the parameter file name: ");      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     scanf("%s",pathtot);    }
   }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   else{    for (i=1;i<=nlstate;i++)
     strcpy(pathtot,argv[1]);      for(j=1;j<=nlstate+ndeath;j++)
   }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    fprintf(ficrespow,"\n");
   /*cygwin_split_path(pathtot,path,optionfile);  #ifdef POWELL
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    powell(p,xi,npar,ftol,&iter,&fret,func);
   /* cutv(path,optionfile,pathtot,'\\');*/  #endif
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  #ifdef NLOPT
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  #ifdef NEWUOA
   chdir(path);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   replace(pathc,path);  #else
     opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
 /*-------- arguments in the command line --------*/  #endif
     lb=vector(0,npar-1);
   strcpy(fileres,"r");    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   strcat(fileres, optionfilefiname);    nlopt_set_lower_bounds(opt, lb);
   strcat(fileres,".txt");    /* Other files have txt extension */    nlopt_set_initial_step1(opt, 0.1);
     
   /*---------arguments file --------*/    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     d->function = func;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     printf("Problem with optionfile %s\n",optionfile);    nlopt_set_min_objective(opt, myfunc, d);
     goto end;    nlopt_set_xtol_rel(opt, ftol);
   }    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
   strcpy(filereso,"o");    }
   strcat(filereso,fileres);    else {
   if((ficparo=fopen(filereso,"w"))==NULL) {      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
   }      iter=1; /* not equal */
     }
   /* Reads comments: lines beginning with '#' */    nlopt_destroy(opt);
   while((c=getc(ficpar))=='#' && c!= EOF){  #endif
     ungetc(c,ficpar);    free_matrix(xi,1,npar,1,npar);
     fgets(line, MAXLINE, ficpar);    fclose(ficrespow);
     puts(line);    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fputs(line,ficparo);    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   }    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   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);  /**** Computes Hessian and covariance matrix ***/
   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);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 while((c=getc(ficpar))=='#' && c!= EOF){  {
     ungetc(c,ficpar);    double  **a,**y,*x,pd;
     fgets(line, MAXLINE, ficpar);    double **hess;
     puts(line);    int i, j;
     fputs(line,ficparo);    int *indx;
   }  
   ungetc(c,ficpar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
      double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
        void lubksb(double **a, int npar, int *indx, double b[]) ;
   covar=matrix(0,NCOVMAX,1,n);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   cptcovn=0;    double gompertz(double p[]);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    hess=matrix(1,npar,1,npar);
   
   ncovmodel=2+cptcovn;    printf("\nCalculation of the hessian matrix. Wait...\n");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
      for (i=1;i<=npar;i++){
   /* Read guess parameters */      printf("%d",i);fflush(stdout);
   /* Reads comments: lines beginning with '#' */      fprintf(ficlog,"%d",i);fflush(ficlog);
   while((c=getc(ficpar))=='#' && c!= EOF){     
     ungetc(c,ficpar);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      /*  printf(" %f ",p[i]);
     fputs(line,ficparo);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   }    }
   ungetc(c,ficpar);    
      for (i=1;i<=npar;i++) {
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for (j=1;j<=npar;j++)  {
     for(i=1; i <=nlstate; i++)        if (j>i) { 
     for(j=1; j <=nlstate+ndeath-1; j++){          printf(".%d%d",i,j);fflush(stdout);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       fprintf(ficparo,"%1d%1d",i1,j1);          hess[i][j]=hessij(p,delti,i,j,func,npar);
       printf("%1d%1d",i,j);          
       for(k=1; k<=ncovmodel;k++){          hess[j][i]=hess[i][j];    
         fscanf(ficpar," %lf",&param[i][j][k]);          /*printf(" %lf ",hess[i][j]);*/
         printf(" %lf",param[i][j][k]);        }
         fprintf(ficparo," %lf",param[i][j][k]);      }
       }    }
       fscanf(ficpar,"\n");    printf("\n");
       printf("\n");    fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");  
     }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    
     a=matrix(1,npar,1,npar);
   p=param[1][1];    y=matrix(1,npar,1,npar);
      x=vector(1,npar);
   /* Reads comments: lines beginning with '#' */    indx=ivector(1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1;i<=npar;i++)
     ungetc(c,ficpar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     fgets(line, MAXLINE, ficpar);    ludcmp(a,npar,indx,&pd);
     puts(line);  
     fputs(line,ficparo);    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   ungetc(c,ficpar);      x[j]=1;
       lubksb(a,npar,indx,x);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for (i=1;i<=npar;i++){ 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        matcov[i][j]=x[i];
   for(i=1; i <=nlstate; i++){      }
     for(j=1; j <=nlstate+ndeath-1; j++){    }
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    printf("\n#Hessian matrix#\n");
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficlog,"\n#Hessian matrix#\n");
       for(k=1; k<=ncovmodel;k++){    for (i=1;i<=npar;i++) { 
         fscanf(ficpar,"%le",&delti3[i][j][k]);      for (j=1;j<=npar;j++) { 
         printf(" %le",delti3[i][j][k]);        printf("%.3e ",hess[i][j]);
         fprintf(ficparo," %le",delti3[i][j][k]);        fprintf(ficlog,"%.3e ",hess[i][j]);
       }      }
       fscanf(ficpar,"\n");      printf("\n");
       printf("\n");      fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");    }
     }  
   }    /* Recompute Inverse */
   delti=delti3[1][1];    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   /* Reads comments: lines beginning with '#' */    ludcmp(a,npar,indx,&pd);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    /*  printf("\n#Hessian matrix recomputed#\n");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    for (j=1;j<=npar;j++) {
     fputs(line,ficparo);      for (i=1;i<=npar;i++) x[i]=0;
   }      x[j]=1;
   ungetc(c,ficpar);      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   matcov=matrix(1,npar,1,npar);        y[i][j]=x[i];
   for(i=1; i <=npar; i++){        printf("%.3e ",y[i][j]);
     fscanf(ficpar,"%s",&str);        fprintf(ficlog,"%.3e ",y[i][j]);
     printf("%s",str);      }
     fprintf(ficparo,"%s",str);      printf("\n");
     for(j=1; j <=i; j++){      fprintf(ficlog,"\n");
       fscanf(ficpar," %le",&matcov[i][j]);    }
       printf(" %.5le",matcov[i][j]);    */
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }    free_matrix(a,1,npar,1,npar);
     fscanf(ficpar,"\n");    free_matrix(y,1,npar,1,npar);
     printf("\n");    free_vector(x,1,npar);
     fprintf(ficparo,"\n");    free_ivector(indx,1,npar);
   }    free_matrix(hess,1,npar,1,npar);
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];  }
      
   printf("\n");  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
     /*-------- Rewriting paramater file ----------*/    int i;
      strcpy(rfileres,"r");    /* "Rparameterfile */    int l=1, lmax=20;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    double k1,k2;
      strcat(rfileres,".");    /* */    double p2[MAXPARM+1]; /* identical to x */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    double res;
     if((ficres =fopen(rfileres,"w"))==NULL) {    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    double fx;
     }    int k=0,kmax=10;
     fprintf(ficres,"#%s\n",version);    double l1;
      
     /*-------- data file ----------*/    fx=func(x);
     if((fic=fopen(datafile,"r"))==NULL)    {    for (i=1;i<=npar;i++) p2[i]=x[i];
       printf("Problem with datafile: %s\n", datafile);goto end;    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
     }      l1=pow(10,l);
       delts=delt;
     n= lastobs;      for(k=1 ; k <kmax; k=k+1){
     severity = vector(1,maxwav);        delt = delta*(l1*k);
     outcome=imatrix(1,maxwav+1,1,n);        p2[theta]=x[theta] +delt;
     num=ivector(1,n);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
     moisnais=vector(1,n);        p2[theta]=x[theta]-delt;
     annais=vector(1,n);        k2=func(p2)-fx;
     moisdc=vector(1,n);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     andc=vector(1,n);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     agedc=vector(1,n);        
     cod=ivector(1,n);  #ifdef DEBUGHESS
     weight=vector(1,n);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        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);
     mint=matrix(1,maxwav,1,n);  #endif
     anint=matrix(1,maxwav,1,n);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     s=imatrix(1,maxwav+1,1,n);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     adl=imatrix(1,maxwav+1,1,n);              k=kmax;
     tab=ivector(1,NCOVMAX);        }
     ncodemax=ivector(1,8);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10;
     i=1;        }
     while (fgets(line, MAXLINE, fic) != NULL)    {        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       if ((i >= firstobs) && (i <=lastobs)) {          delts=delt;
                }
         for (j=maxwav;j>=1;j--){      }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    }
           strcpy(line,stra);    delti[theta]=delts;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    return res; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    
         }  }
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  {
     int i;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    int l=1, lmax=20;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    double k1,k2,k3,k4,res,fx;
     double p2[MAXPARM+1];
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    int k;
         for (j=ncovcol;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fx=func(x);
         }    for (k=1; k<=2; k++) {
         num[i]=atol(stra);      for (i=1;i<=npar;i++) p2[i]=x[i];
              p2[thetai]=x[thetai]+delti[thetai]/k;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           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;}*/      k1=func(p2)-fx;
     
         i=i+1;      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     }      k2=func(p2)-fx;
     /* printf("ii=%d", ij);    
        scanf("%d",i);*/      p2[thetai]=x[thetai]-delti[thetai]/k;
   imx=i-1; /* Number of individuals */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
   /* for (i=1; i<=imx; i++){    
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      p2[thetai]=x[thetai]-delti[thetai]/k;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      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
   /* for (i=1; i<=imx; i++){      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);
      if (s[4][i]==9)  s[4][i]=-1;      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);
      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]));}  #endif
   */    }
      return res;
   /* Calculation of the number of parameter from char model*/  }
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);  /************** Inverse of matrix **************/
   Tvaraff=ivector(1,15);  void ludcmp(double **a, int n, int *indx, double *d) 
   Tvard=imatrix(1,15,1,2);  { 
   Tage=ivector(1,15);          int i,imax,j,k; 
        double big,dum,sum,temp; 
   if (strlen(model) >1){    double *vv; 
     j=0, j1=0, k1=1, k2=1;   
     j=nbocc(model,'+');    vv=vector(1,n); 
     j1=nbocc(model,'*');    *d=1.0; 
     cptcovn=j+1;    for (i=1;i<=n;i++) { 
     cptcovprod=j1;      big=0.0; 
          for (j=1;j<=n;j++) 
     strcpy(modelsav,model);        if ((temp=fabs(a[i][j])) > big) big=temp; 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       printf("Error. Non available option model=%s ",model);      vv[i]=1.0/big; 
       goto end;    } 
     }    for (j=1;j<=n;j++) { 
          for (i=1;i<j;i++) { 
     for(i=(j+1); i>=1;i--){        sum=a[i][j]; 
       cutv(stra,strb,modelsav,'+');        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        a[i][j]=sum; 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      } 
       /*scanf("%d",i);*/      big=0.0; 
       if (strchr(strb,'*')) {      for (i=j;i<=n;i++) { 
         cutv(strd,strc,strb,'*');        sum=a[i][j]; 
         if (strcmp(strc,"age")==0) {        for (k=1;k<j;k++) 
           cptcovprod--;          sum -= a[i][k]*a[k][j]; 
           cutv(strb,stre,strd,'V');        a[i][j]=sum; 
           Tvar[i]=atoi(stre);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           cptcovage++;          big=dum; 
             Tage[cptcovage]=i;          imax=i; 
             /*printf("stre=%s ", stre);*/        } 
         }      } 
         else if (strcmp(strd,"age")==0) {      if (j != imax) { 
           cptcovprod--;        for (k=1;k<=n;k++) { 
           cutv(strb,stre,strc,'V');          dum=a[imax][k]; 
           Tvar[i]=atoi(stre);          a[imax][k]=a[j][k]; 
           cptcovage++;          a[j][k]=dum; 
           Tage[cptcovage]=i;        } 
         }        *d = -(*d); 
         else {        vv[imax]=vv[j]; 
           cutv(strb,stre,strc,'V');      } 
           Tvar[i]=ncovcol+k1;      indx[j]=imax; 
           cutv(strb,strc,strd,'V');      if (a[j][j] == 0.0) a[j][j]=TINY; 
           Tprod[k1]=i;      if (j != n) { 
           Tvard[k1][1]=atoi(strc);        dum=1.0/(a[j][j]); 
           Tvard[k1][2]=atoi(stre);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           Tvar[cptcovn+k2]=Tvard[k1][1];      } 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    } 
           for (k=1; k<=lastobs;k++)    free_vector(vv,1,n);  /* Doesn't work */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  ;
           k1++;  } 
           k2=k2+2;  
         }  void lubksb(double **a, int n, int *indx, double b[]) 
       }  { 
       else {    int i,ii=0,ip,j; 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double sum; 
        /*  scanf("%d",i);*/   
       cutv(strd,strc,strb,'V');    for (i=1;i<=n;i++) { 
       Tvar[i]=atoi(strc);      ip=indx[i]; 
       }      sum=b[ip]; 
       strcpy(modelsav,stra);        b[ip]=b[i]; 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      if (ii) 
         scanf("%d",i);*/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     }      else if (sum) ii=i; 
 }      b[i]=sum; 
      } 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    for (i=n;i>=1;i--) { 
   printf("cptcovprod=%d ", cptcovprod);      sum=b[i]; 
   scanf("%d ",i);*/      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     fclose(fic);      b[i]=sum/a[i][i]; 
     } 
     /*  if(mle==1){*/  } 
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;  void pstamp(FILE *fichier)
     }  {
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     agev=matrix(1,maxwav,1,imx);  }
   
     for (i=1; i<=imx; i++) {  /************ Frequencies ********************/
       for(m=2; (m<= maxwav); m++) {  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[])
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  {  /* Some frequencies */
          anint[m][i]=9999;    
          s[m][i]=-1;    int i, m, jk, j1, bool, z1,j;
        }    int first;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    double ***freq; /* Frequencies */
       }    double *pp, **prop;
     }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
     for (i=1; i<=imx; i++)  {    
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    pp=vector(1,nlstate);
       for(m=1; (m<= maxwav); m++){    prop=matrix(1,nlstate,iagemin,iagemax+3);
         if(s[m][i] >0){    strcpy(fileresp,"p");
           if (s[m][i] >= nlstate+1) {    strcat(fileresp,fileres);
             if(agedc[i]>0)    if((ficresp=fopen(fileresp,"w"))==NULL) {
               if(moisdc[i]!=99 && andc[i]!=9999)      printf("Problem with prevalence resultfile: %s\n", fileresp);
                 agev[m][i]=agedc[i];      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      exit(0);
            else {    }
               if (andc[i]!=9999){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    j1=0;
               agev[m][i]=-1;    
               }    j=cptcoveff;
             }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    first=1;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
               agev[m][i]=1;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
             else if(agev[m][i] <agemin){    /*    j1++; */
               agemin=agev[m][i];    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
             }          scanf("%d", i);*/
             else if(agev[m][i] >agemax){        for (i=-5; i<=nlstate+ndeath; i++)  
               agemax=agev[m][i];          for (jk=-5; jk<=nlstate+ndeath; jk++)  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            for(m=iagemin; m <= iagemax+3; m++)
             }              freq[i][jk][m]=0;
             /*agev[m][i]=anint[m][i]-annais[i];*/        
             /*   agev[m][i] = age[i]+2*m;*/        for (i=1; i<=nlstate; i++)  
           }          for(m=iagemin; m <= iagemax+3; m++)
           else { /* =9 */            prop[i][m]=0;
             agev[m][i]=1;        
             s[m][i]=-1;        dateintsum=0;
           }        k2cpt=0;
         }        for (i=1; i<=imx; i++) {
         else /*= 0 Unknown */          bool=1;
           agev[m][i]=1;          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
       }            for (z1=1; z1<=cptcoveff; z1++)       
                  if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
     }                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
     for (i=1; i<=imx; i++)  {                bool=0;
       for(m=1; (m<= maxwav); m++){                /* 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", 
         if (s[m][i] > (nlstate+ndeath)) {                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
           printf("Error: Wrong value in nlstate or ndeath\n");                    j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
           goto end;                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
         }              } 
       }          }
     }   
           if (bool==1){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
     free_vector(severity,1,maxwav);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     free_imatrix(outcome,1,maxwav+1,1,n);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     free_vector(moisnais,1,n);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     free_vector(annais,1,n);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     /* free_matrix(mint,1,maxwav,1,n);                if (m<lastpass) {
        free_matrix(anint,1,maxwav,1,n);*/                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     free_vector(moisdc,1,n);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     free_vector(andc,1,n);                }
                 
                    if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     wav=ivector(1,imx);                  dateintsum=dateintsum+k2;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                  k2cpt++;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                }
                    /*}*/
     /* Concatenates waves */            }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          }
         } /* end i */
          
       Tcode=ivector(1,100);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        pstamp(ficresp);
       ncodemax[1]=1;        if  (cptcovn>0) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          fprintf(ficresp, "\n#********** Variable "); 
                for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    codtab=imatrix(1,100,1,10);          fprintf(ficresp, "**********\n#");
    h=0;          fprintf(ficlog, "\n#********** Variable "); 
    m=pow(2,cptcoveff);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficlog, "**********\n#");
    for(k=1;k<=cptcoveff; k++){        }
      for(i=1; i <=(m/pow(2,k));i++){        for(i=1; i<=nlstate;i++) 
        for(j=1; j <= ncodemax[k]; j++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        fprintf(ficresp, "\n");
            h++;        
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        for(i=iagemin; i <= iagemax+3; i++){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          if(i==iagemax+3){
          }            fprintf(ficlog,"Total");
        }          }else{
      }            if(first==1){
    }              first=0;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);              printf("See log file for details...\n");
       codtab[1][2]=1;codtab[2][2]=2; */            }
    /* for(i=1; i <=m ;i++){            fprintf(ficlog,"Age %d", i);
       for(k=1; k <=cptcovn; k++){          }
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       printf("\n");              pp[jk] += freq[jk][m][i]; 
       }          }
       scanf("%d",i);*/          for(jk=1; jk <=nlstate ; jk++){
                for(m=-1, pos=0; m <=0 ; m++)
    /* Calculates basic frequencies. Computes observed prevalence at single age              pos += freq[jk][m][i];
        and prints on file fileres'p'. */            if(pp[jk]>=1.e-10){
               if(first==1){
                    printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }else{
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if(first==1)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                  }
     /* 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) */          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     if(mle==1){              pp[jk] += freq[jk][m][i];
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          }       
     }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                pos += pp[jk];
     /*--------- results files --------------*/            posprop += prop[jk][i];
     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(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
    jk=1;              if(first==1)
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    for(i=1,jk=1; i <=nlstate; i++){            }else{
      for(k=1; k <=(nlstate+ndeath); k++){              if(first==1)
        if (k != i)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
          {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
            printf("%d%d ",i,k);            }
            fprintf(ficres,"%1d%1d ",i,k);            if( i <= iagemax){
            for(j=1; j <=ncovmodel; j++){              if(pos>=1.e-5){
              printf("%f ",p[jk]);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
              fprintf(ficres,"%f ",p[jk]);                /*probs[i][jk][j1]= pp[jk]/pos;*/
              jk++;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
            }              }
            printf("\n");              else
            fprintf(ficres,"\n");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
          }            }
      }          }
    }          
  if(mle==1){          for(jk=-1; jk <=nlstate+ndeath; jk++)
     /* Computing hessian and covariance matrix */            for(m=-1; m <=nlstate+ndeath; m++)
     ftolhess=ftol; /* Usually correct */              if(freq[jk][m][i] !=0 ) {
     hesscov(matcov, p, npar, delti, ftolhess, func);              if(first==1)
  }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     printf("# Scales (for hessian or gradient estimation)\n");              }
      for(i=1,jk=1; i <=nlstate; i++){          if(i <= iagemax)
       for(j=1; j <=nlstate+ndeath; j++){            fprintf(ficresp,"\n");
         if (j!=i) {          if(first==1)
           fprintf(ficres,"%1d%1d",i,j);            printf("Others in log...\n");
           printf("%1d%1d",i,j);          fprintf(ficlog,"\n");
           for(k=1; k<=ncovmodel;k++){        }
             printf(" %.5e",delti[jk]);        /*}*/
             fprintf(ficres," %.5e",delti[jk]);    }
             jk++;    dateintmean=dateintsum/k2cpt; 
           }   
           printf("\n");    fclose(ficresp);
           fprintf(ficres,"\n");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         }    free_vector(pp,1,nlstate);
       }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      }    /* End of Freq */
      }
     k=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");  /************ Prevalence ********************/
     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");  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)
     for(i=1;i<=npar;i++){  {  
       /*  if (k>nlstate) k=1;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       i1=(i-1)/(ncovmodel*nlstate)+1;       in each health status at the date of interview (if between dateprev1 and dateprev2).
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);       We still use firstpass and lastpass as another selection.
       printf("%s%d%d",alph[k],i1,tab[i]);*/    */
       fprintf(ficres,"%3d",i);   
       printf("%3d",i);    int i, m, jk, j1, bool, z1,j;
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);    double **prop;
         printf(" %.5e",matcov[i][j]);    double posprop; 
       }    double  y2; /* in fractional years */
       fprintf(ficres,"\n");    int iagemin, iagemax;
       printf("\n");    int first; /** to stop verbosity which is redirected to log file */
       k++;  
     }    iagemin= (int) agemin;
        iagemax= (int) agemax;
     while((c=getc(ficpar))=='#' && c!= EOF){    /*pp=vector(1,nlstate);*/
       ungetc(c,ficpar);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       fgets(line, MAXLINE, ficpar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       puts(line);    j1=0;
       fputs(line,ficparo);    
     }    /*j=cptcoveff;*/
     ungetc(c,ficpar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     estepm=0;    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    first=1;
     if (estepm==0 || estepm < stepm) estepm=stepm;    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
     if (fage <= 2) {      /*for(i1=1; i1<=ncodemax[k1];i1++){
       bage = ageminpar;        j1++;*/
       fage = agemaxpar;        
     }        for (i=1; i<=nlstate; i++)  
              for(m=iagemin; m <= iagemax+3; m++)
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            prop[i][m]=0.0;
     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);        for (i=1; i<=imx; i++) { /* Each individual */
            bool=1;
     while((c=getc(ficpar))=='#' && c!= EOF){          if  (cptcovn>0) {
     ungetc(c,ficpar);            for (z1=1; z1<=cptcoveff; z1++) 
     fgets(line, MAXLINE, ficpar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     puts(line);                bool=0;
     fputs(line,ficparo);          } 
   }          if (bool==1) { 
   ungetc(c,ficpar);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                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); 
   while((c=getc(ficpar))=='#' && c!= EOF){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     ungetc(c,ficpar);                  /*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]]);*/
     fgets(line, MAXLINE, ficpar);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     puts(line);                  prop[s[m][i]][iagemax+3] += weight[i]; 
     fputs(line,ficparo);                } 
   }              }
   ungetc(c,ficpar);            } /* end selection of waves */
            }
         }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        for(i=iagemin; i <= iagemax+3; i++){  
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
   fscanf(ficpar,"pop_based=%d\n",&popbased);          } 
   fprintf(ficparo,"pop_based=%d\n",popbased);            
   fprintf(ficres,"pop_based=%d\n",popbased);            for(jk=1; jk <=nlstate ; jk++){     
              if( i <=  iagemax){ 
   while((c=getc(ficpar))=='#' && c!= EOF){              if(posprop>=1.e-5){ 
     ungetc(c,ficpar);                probs[i][jk][j1]= prop[jk][i]/posprop;
     fgets(line, MAXLINE, ficpar);              } else{
     puts(line);                if(first==1){
     fputs(line,ficparo);                  first=0;
   }                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
   ungetc(c,ficpar);                }
               }
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);            } 
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          }/* end jk */ 
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        }/* end i */ 
       /*} *//* end i1 */
     } /* end j1 */
 while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     fgets(line, MAXLINE, ficpar);    /*free_vector(pp,1,nlstate);*/
     puts(line);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     fputs(line,ficparo);  }  /* End of prevalence */
   }  
   ungetc(c,ficpar);  /************* Waves Concatenation ***************/
   
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  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)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  {
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 /*------------ gnuplot -------------*/       and mw[mi+1][i]. dh depends on stepm.
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);       */
    
 /*------------ free_vector  -------------*/    int i, mi, m;
  chdir(path);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         double sum=0., jmean=0.;*/
  free_ivector(wav,1,imx);    int first;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    int j, k=0,jk, ju, jl;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      double sum=0.;
  free_ivector(num,1,n);    first=0;
  free_vector(agedc,1,n);    jmin=100000;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    jmax=-1;
  fclose(ficparo);    jmean=0.;
  fclose(ficres);    for(i=1; i<=imx; i++){
       mi=0;
 /*--------- index.htm --------*/      m=firstpass;
       while(s[m][i] <= nlstate){
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           mw[++mi][i]=m;
          if(m >=lastpass)
   /*--------------- Prevalence limit --------------*/          break;
          else
   strcpy(filerespl,"pl");          m++;
   strcat(filerespl,fileres);      }/* end while */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      if (s[m][i] > nlstate){
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        mi++;     /* Death is another wave */
   }        /* if(mi==0)  never been interviewed correctly before death */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);           /* Only death is a correct wave */
   fprintf(ficrespl,"#Prevalence limit\n");        mw[mi][i]=m;
   fprintf(ficrespl,"#Age ");      }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");      wav[i]=mi;
        if(mi==0){
   prlim=matrix(1,nlstate,1,nlstate);        nbwarn++;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if(first==0){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          first=1;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        if(first==1){
   k=0;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   agebase=ageminpar;        }
   agelim=agemaxpar;      } /* end mi==0 */
   ftolpl=1.e-10;    } /* End individuals */
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
   for(cptcov=1;cptcov<=i1;cptcov++){        if (stepm <=0)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          dh[mi][i]=1;
         k=k+1;        else{
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         fprintf(ficrespl,"\n#******");            if (agedc[i] < 2*AGESUP) {
         for(j=1;j<=cptcoveff;j++)              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              if(j==0) j=1;  /* Survives at least one month after exam */
         fprintf(ficrespl,"******\n");              else if(j<0){
                        nberr++;
         for (age=agebase; age<=agelim; age++){                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]);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                j=1; /* Temporary Dangerous patch */
           fprintf(ficrespl,"%.0f",age );                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           for(i=1; i<=nlstate;i++)                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(ficrespl," %.5f", prlim[i][i]);                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);
           fprintf(ficrespl,"\n");              }
         }              k=k+1;
       }              if (j >= jmax){
     }                jmax=j;
   fclose(ficrespl);                ijmax=i;
               }
   /*------------- h Pij x at various ages ------------*/              if (j <= jmin){
                  jmin=j;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                ijmin=i;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;              sum=sum+j;
   }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   printf("Computing pij: result on file '%s' \n", filerespij);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }
   /*if (stepm<=24) stepsize=2;*/          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   agelim=AGESUP;  /*        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]); */
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            k=k+1;
              if (j >= jmax) {
   k=0;              jmax=j;
   for(cptcov=1;cptcov<=i1;cptcov++){              ijmax=i;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            }
       k=k+1;            else if (j <= jmin){
         fprintf(ficrespij,"\n#****** ");              jmin=j;
         for(j=1;j<=cptcoveff;j++)              ijmin=i;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
         fprintf(ficrespij,"******\n");            /*        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]);*/
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            if(j<0){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              nberr++;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              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]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              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]);
           oldm=oldms;savm=savms;            }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              sum=sum+j;
           fprintf(ficrespij,"# Age");          }
           for(i=1; i<=nlstate;i++)          jk= j/stepm;
             for(j=1; j<=nlstate+ndeath;j++)          jl= j -jk*stepm;
               fprintf(ficrespij," %1d-%1d",i,j);          ju= j -(jk+1)*stepm;
           fprintf(ficrespij,"\n");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           for (h=0; h<=nhstepm; h++){            if(jl==0){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );              dh[mi][i]=jk;
             for(i=1; i<=nlstate;i++)              bh[mi][i]=0;
               for(j=1; j<=nlstate+ndeath;j++)            }else{ /* We want a negative bias in order to only have interpolation ie
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                    * to avoid the price of an extra matrix product in likelihood */
             fprintf(ficrespij,"\n");              dh[mi][i]=jk+1;
           }              bh[mi][i]=ju;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
           fprintf(ficrespij,"\n");          }else{
         }            if(jl <= -ju){
     }              dh[mi][i]=jk;
   }              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                                   */
             }
   fclose(ficrespij);            else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   /*---------- Forecasting ------------------*/            }
   if((stepm == 1) && (strcmp(model,".")==0)){            if(dh[mi][i]==0){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);              dh[mi][i]=1; /* At least one step */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);              bh[mi][i]=ju; /* At least one step */
     free_matrix(mint,1,maxwav,1,n);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);            }
     free_vector(weight,1,n);}          } /* end if mle */
   else{        }
     erreur=108;      } /* end wave */
     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);    }
   }    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);
     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);
   /*---------- Health expectancies and variances ------------*/   }
   
   strcpy(filerest,"t");  /*********** Tricode ****************************/
   strcat(filerest,fileres);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   if((ficrest=fopen(filerest,"w"))==NULL) {  {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   }    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);     * Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
      * nbcode[Tvar[j]][1]= 
   strcpy(filerese,"e");    */
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    int modmaxcovj=0; /* Modality max of covariates j */
   }    int cptcode=0; /* Modality max of covariates j */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    int modmincovj=0; /* Modality min of covariates j */
   
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);    cptcoveff=0; 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   }    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
     /* Loop on covariates without age and products */
   k=0;    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
   for(cptcov=1;cptcov<=i1;cptcov++){      for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                                 modality of this covariate Vj*/ 
       k=k+1;        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
       fprintf(ficrest,"\n#****** ");                                      * If product of Vn*Vm, still boolean *:
       for(j=1;j<=cptcoveff;j++)                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
       fprintf(ficrest,"******\n");        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
       fprintf(ficreseij,"\n#****** ");        if (ij > modmaxcovj)
       for(j=1;j<=cptcoveff;j++)          modmaxcovj=ij; 
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        else if (ij < modmincovj) 
       fprintf(ficreseij,"******\n");          modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
       fprintf(ficresvij,"\n#****** ");          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
       for(j=1;j<=cptcoveff;j++)          exit(1);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }else
       fprintf(ficresvij,"******\n");        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       oldm=oldms;savm=savms;        /* getting the maximum value of the modality of the covariate
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);             (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);           female is 1, then modmaxcovj=1.*/
       oldm=oldms;savm=savms;      } /* end for loop on individuals */
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
          cptcode=modmaxcovj;
       /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       /*for (i=0; i<=cptcode; i++) {*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
       fprintf(ficrest,"\n");        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
       epj=vector(1,nlstate+1);        }
       for(age=bage; age <=fage ;age++){        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
         if (popbased==1) {      } /* Ndum[-1] number of undefined modalities */
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][k];      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
         }      /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
                 If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
         fprintf(ficrest," %4.0f",age);         modmincovj=3; modmaxcovj = 7;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){         There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
           for(i=1, epj[j]=0.;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;
             epj[j] += prlim[i][i]*eij[i][j][(int)age];         defining two dummy variables: variables V1_1 and V1_2.
           }         nbcode[Tvar[j]][ij]=k;
           epj[nlstate+1] +=epj[j];         nbcode[Tvar[j]][1]=0;
         }         nbcode[Tvar[j]][2]=1;
         for(i=1, vepp=0.;i <=nlstate;i++)         nbcode[Tvar[j]][3]=2;
           for(j=1;j <=nlstate;j++)      */
             vepp += vareij[i][j][(int)age];      ij=1; /* ij is similar to i but can jumps over null modalities */
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         for(j=1;j <=nlstate;j++){        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));          /*recode from 0 */
         }          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
         fprintf(ficrest,"\n");            nbcode[Tvar[j]][ij]=k;  /* stores the modality k in an array nbcode. 
       }                                       k is a modality. If we have model=V1+V1*sex 
     }                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   }            ij++;
           }
   fclose(ficreseij);          if (ij > ncodemax[j]) break; 
   fclose(ficresvij);        }  /* end of loop on */
   fclose(ficrest);      } /* end of loop on modality */ 
   fclose(ficpar);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   free_vector(epj,1,nlstate+1);    
     for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   /*------- Variance limit prevalence------*/      
     for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
   strcpy(fileresvpl,"vpl");     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   strcat(fileresvpl,fileres);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {     Ndum[ij]++; /* Might be supersed V1 + V1*age */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);   } 
     exit(0);  
   }   ij=1;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   k=0;     if((Ndum[i]!=0) && (i<=ncovcol)){
   for(cptcov=1;cptcov<=i1;cptcov++){       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       Tvaraff[ij]=i; /*For printing (unclear) */
       k=k+1;       ij++;
       fprintf(ficresvpl,"\n#****** ");     }else
       for(j=1;j<=cptcoveff;j++)         Tvaraff[ij]=0;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   }
       fprintf(ficresvpl,"******\n");   ij--;
         cptcoveff=ij; /*Number of total covariates*/
       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);  
     }  
  }  /*********** Health Expectancies ****************/
   
   fclose(ficresvpl);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
   /*---------- End : free ----------------*/  {
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    /* Health expectancies, no variances */
      int i, j, nhstepm, hstepm, h, nstepm;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    int nhstepma, nstepma; /* Decreasing with age */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double age, agelim, hf;
      double ***p3mat;
      double eip;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    pstamp(ficreseij);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficreseij,"# Age");
      for(i=1; i<=nlstate;i++){
   free_matrix(matcov,1,npar,1,npar);      for(j=1; j<=nlstate;j++){
   free_vector(delti,1,npar);        fprintf(ficreseij," e%1d%1d ",i,j);
   free_matrix(agev,1,maxwav,1,imx);      }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      fprintf(ficreseij," e%1d. ",i);
     }
   if(erreur >0)    fprintf(ficreseij,"\n");
     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 */    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   /* 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);*/    else  hstepm=estepm;   
   /*------ End -----------*/    /* 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
  end:     * we are calculating an estimate of the Life Expectancy assuming a linear 
 #ifdef windows     * progression in between and thus overestimating or underestimating according
   /* chdir(pathcd);*/     * to the curvature of the survival function. If, for the same date, we 
 #endif     * estimate the model with stepm=1 month, we can keep estepm to 24 months
  /*system("wgnuplot graph.plt");*/     * to compare the new estimate of Life expectancy with the same linear 
  /*system("../gp37mgw/wgnuplot graph.plt");*/     * hypothesis. A more precise result, taking into account a more precise
  /*system("cd ../gp37mgw");*/     * curvature will be obtained if estepm is as small as stepm. */
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    /* For example we decided to compute the life expectancy with the smallest unit */
  strcat(plotcmd," ");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  strcat(plotcmd,optionfilegnuplot);       nhstepm is the number of hstepm from age to agelim 
  system(plotcmd);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
 #ifdef windows       and note for a fixed period like estepm months */
   while (z[0] != 'q') {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     /* chdir(path); */       survival function given by stepm (the optimization length). Unfortunately it
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");       means that if the survival funtion is printed only each two years of age and if
     scanf("%s",z);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     if (z[0] == 'c') system("./imach");       results. So we changed our mind and took the option of the best precision.
     else if (z[0] == 'e') system(optionfilehtm);    */
     else if (z[0] == 'g') system(plotcmd);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     else if (z[0] == 'q') exit(0);  
   }    agelim=AGESUP;
 #endif    /* 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 */
       
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     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 */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       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] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
   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[] )
   
   {
     /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     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]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     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()
    {
      /* #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-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           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;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
   
     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();
   
     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 choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) { /* Main Wizard */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*  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 */
   
     /* 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]));
   
       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);
       }
       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(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(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.1.36  
changed lines
  Added in v.1.190


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