Diff for /imach/src/imach.c between versions 1.25 and 1.184

version 1.25, 2002/02/26 17:11:54 version 1.184, 2015/03/11 11:52:39
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.184  2015/03/11 11:52:39  brouard
      Summary: Back from Windows 8. Intel Compiler
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.183  2015/03/10 20:34:32  brouard
   first survey ("cross") where individuals from different ages are    Summary: 0.98q0, trying with directest, mnbrak fixed
   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    We use directest instead of original Powell test; probably no
   second wave of interviews ("longitudinal") which measure each change    incidence on the results, but better justifications;
   (if any) in individual health status.  Health expectancies are    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   computed from the time spent in each health state according to a    wrong results.
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.182  2015/02/12 08:19:57  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: Trying to keep directest which seems simpler and more general
   probabibility to be observed in state j at the second wave    Author: Nicolas Brouard
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.181  2015/02/11 23:22:24  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Summary: Comments on Powell added
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Author:
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.180  2015/02/11 17:33:45  brouard
     Summary: Finishing move from main to function (hpijx and prevalence_limit)
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.179  2015/01/04 09:57:06  brouard
   identical for each individual. Also, if a individual missed an    Summary: back to OS/X
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.178  2015/01/04 09:35:48  brouard
     *** empty log message ***
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.177  2015/01/03 18:40:56  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: Still testing ilc32 on OSX
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.176  2015/01/03 16:45:04  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    *** empty log message ***
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.174  2015/01/03 16:15:49  brouard
      Summary: Still in cross-compilation
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.173  2015/01/03 12:06:26  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: trying to detect cross-compilation
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.172  2014/12/27 12:07:47  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.171  2014/12/23 13:26:59  brouard
      Summary: Back from Visual C
 #include <math.h>  
 #include <stdio.h>    Still problem with utsname.h on Windows
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.169  2014/12/22 23:08:31  brouard
 #define windows    Summary: 0.98p
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.168  2014/12/22 15:17:42  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: update
   
 #define NINTERVMAX 8    Revision 1.167  2014/12/22 13:50:56  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Summary: Testing uname and compiler version and if compiled 32 or 64
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Testing on Linux 64
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.166  2014/12/22 11:40:47  brouard
 #define AGESUP 130    *** empty log message ***
 #define AGEBASE 40  
     Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
 int erreur; /* Error number */  
 int nvar;    * imach.c (Module): Merging 1.61 to 1.162
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.164  2014/12/16 10:52:11  brouard
 int nlstate=2; /* Number of live states */    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * imach.c (Module): Merging 1.61 to 1.162
 int popbased=0;  
     Revision 1.163  2014/12/16 10:30:11  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    * imach.c (Module): Merging 1.61 to 1.162
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.162  2014/09/25 11:43:39  brouard
 int mle, weightopt;    Summary: temporary backup 0.99!
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.1  2014/09/16 11:06:58  brouard
 double jmean; /* Mean space between 2 waves */    Summary: With some code (wrong) for nlopt
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Author:
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.161  2014/09/15 20:41:41  brouard
 FILE *ficreseij;    Summary: Problem with macro SQR on Intel compiler
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.160  2014/09/02 09:24:05  brouard
   char fileresv[FILENAMELENGTH];    *** empty log message ***
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.159  2014/09/01 10:34:10  brouard
     Summary: WIN32
 #define NR_END 1    Author: Brouard
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
 #define NRANSI  
 #define ITMAX 200    Revision 1.157  2014/08/27 16:26:55  brouard
     Summary: Preparing windows Visual studio version
 #define TOL 2.0e-4    Author: Brouard
   
 #define CGOLD 0.3819660    In order to compile on Visual studio, time.h is now correct and time_t
 #define ZEPS 1.0e-10    and tm struct should be used. difftime should be used but sometimes I
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    just make the differences in raw time format (time(&now).
     Trying to suppress #ifdef LINUX
 #define GOLD 1.618034    Add xdg-open for __linux in order to open default browser.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.155  2014/08/25 18:32:34  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Summary: New compile, minor changes
      Author: Brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.154  2014/06/20 17:32:08  brouard
     Summary: Outputs now all graphs of convergence to period prevalence
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.153  2014/06/20 16:45:46  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Summary: If 3 live state, convergence to period prevalence on same graph
     Author: Brouard
 int imx;  
 int stepm;    Revision 1.152  2014/06/18 17:54:09  brouard
 /* Stepm, step in month: minimum step interpolation*/    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
 int m,nb;    Revision 1.151  2014/06/18 16:43:30  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    *** empty log message ***
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.150  2014/06/18 16:42:35  brouard
 double dateintmean=0;    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
 double *weight;  
 int **s; /* Status */    Revision 1.149  2014/06/18 15:51:14  brouard
 double *agedc, **covar, idx;    Summary: Some fixes in parameter files errors
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Author: Nicolas Brouard
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.148  2014/06/17 17:38:48  brouard
 double ftolhess; /* Tolerance for computing hessian */    Summary: Nothing new
     Author: Brouard
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Just a new packaging for OS/X version 0.98nS
 {  
    char *s;                             /* pointer */    Revision 1.147  2014/06/16 10:33:11  brouard
    int  l1, l2;                         /* length counters */    *** empty log message ***
   
    l1 = strlen( path );                 /* length of path */    Revision 1.146  2014/06/16 10:20:28  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Summary: Merge
 #ifdef windows    Author: Brouard
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Merge, before building revised version.
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.145  2014/06/10 21:23:15  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    Summary: Debugging with valgrind
 #if     defined(__bsd__)                /* get current working directory */    Author: Nicolas Brouard
       extern char       *getwd( );  
     Lot of changes in order to output the results with some covariates
       if ( getwd( dirc ) == NULL ) {    After the Edimburgh REVES conference 2014, it seems mandatory to
 #else    improve the code.
       extern char       *getcwd( );    No more memory valgrind error but a lot has to be done in order to
     continue the work of splitting the code into subroutines.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Also, decodemodel has been improved. Tricode is still not
 #endif    optimal. nbcode should be improved. Documentation has been added in
          return( GLOCK_ERROR_GETCWD );    the source code.
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.143  2014/01/26 09:45:38  brouard
    } else {                             /* strip direcotry from path */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.142  2014/01/26 03:57:36  brouard
       dirc[l1-l2] = 0;                  /* add zero */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    }  
    l1 = strlen( dirc );                 /* length of directory */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.141  2014/01/26 02:42:01  brouard
 #else    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.140  2011/09/02 10:37:54  brouard
    s = strrchr( name, '.' );            /* find last / */    Summary: times.h is ok with mingw32 now.
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.139  2010/06/14 07:50:17  brouard
    l1= strlen( name);    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
    l2= strlen( s)+1;    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.138  2010/04/30 18:19:40  brouard
    return( 0 );                         /* we're done */    *** empty log message ***
 }  
     Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
 /******************************************/    than V1+V2. A lot of change to be done. Unstable.
   
 void replace(char *s, char*t)    Revision 1.136  2010/04/26 20:30:53  brouard
 {    (Module): merging some libgsl code. Fixing computation
   int i;    of likelione (using inter/intrapolation if mle = 0) in order to
   int lg=20;    get same likelihood as if mle=1.
   i=0;    Some cleaning of code and comments added.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.135  2009/10/29 15:33:14  brouard
     (s[i] = t[i]);    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
     if (t[i]== '\\') s[i]='/';  
   }    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.
   
 int nbocc(char *s, char occ)    Revision 1.133  2009/07/06 10:21:25  brouard
 {    just nforces
   int i,j=0;  
   int lg=20;    Revision 1.132  2009/07/06 08:22:05  brouard
   i=0;    Many tings
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.131  2009/06/20 16:22:47  brouard
   if  (s[i] == occ ) j++;    Some dimensions resccaled
   }  
   return j;    Revision 1.130  2009/05/26 06:44:34  brouard
 }    (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
 void cutv(char *u,char *v, char*t, char occ)    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 {  
   int i,lg,j,p=0;    Revision 1.129  2007/08/31 13:49:27  lievre
   i=0;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.128  2006/06/30 13:02:05  brouard
   }    (Module): Clarifications on computing e.j
   
   lg=strlen(t);    Revision 1.127  2006/04/28 18:11:50  brouard
   for(j=0; j<p; j++) {    (Module): Yes the sum of survivors was wrong since
     (u[j] = t[j]);    imach-114 because nhstepm was no more computed in the age
   }    loop. Now we define nhstepma in the age loop.
      u[p]='\0';    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
    for(j=0; j<= lg; j++) {    and then all the health expectancies with variances or standard
     if (j>=(p+1))(v[j-p-1] = t[j]);    deviation (needs data from the Hessian matrices) which slows the
   }    computation.
 }    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 /********************** nrerror ********************/  
     Revision 1.126  2006/04/28 17:23:28  brouard
 void nrerror(char error_text[])    (Module): Yes the sum of survivors was wrong since
 {    imach-114 because nhstepm was no more computed in the age
   fprintf(stderr,"ERREUR ...\n");    loop. Now we define nhstepma in the age loop.
   fprintf(stderr,"%s\n",error_text);    Version 0.98h
   exit(1);  
 }    Revision 1.125  2006/04/04 15:20:31  lievre
 /*********************** vector *******************/    Errors in calculation of health expectancies. Age was not initialized.
 double *vector(int nl, int nh)    Forecasting file added.
 {  
   double *v;    Revision 1.124  2006/03/22 17:13:53  lievre
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Parameters are printed with %lf instead of %f (more numbers after the comma).
   if (!v) nrerror("allocation failure in vector");    The log-likelihood is printed in the log file
   return v-nl+NR_END;  
 }    Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
 /************************ free vector ******************/    name. <head> headers where missing.
 void free_vector(double*v, int nl, int nh)  
 {    * imach.c (Module): Weights can have a decimal point as for
   free((FREE_ARG)(v+nl-NR_END));    English (a comma might work with a correct LC_NUMERIC environment,
 }    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 /************************ivector *******************************/    1.
 int *ivector(long nl,long nh)    Version 0.98g
 {  
   int *v;    Revision 1.122  2006/03/20 09:45:41  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): Weights can have a decimal point as for
   if (!v) nrerror("allocation failure in ivector");    English (a comma might work with a correct LC_NUMERIC environment,
   return v-nl+NR_END;    otherwise the weight is truncated).
 }    Modification of warning when the covariates values are not 0 or
     1.
 /******************free ivector **************************/    Version 0.98g
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.121  2006/03/16 17:45:01  lievre
   free((FREE_ARG)(v+nl-NR_END));    * imach.c (Module): Comments concerning covariates added
 }  
     * imach.c (Module): refinements in the computation of lli if
 /******************* imatrix *******************************/    status=-2 in order to have more reliable computation if stepm is
 int **imatrix(long nrl, long nrh, long ncl, long nch)    not 1 month. Version 0.98f
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Revision 1.120  2006/03/16 15:10:38  lievre
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Module): refinements in the computation of lli if
   int **m;    status=-2 in order to have more reliable computation if stepm is
      not 1 month. Version 0.98f
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.119  2006/03/15 17:42:26  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Bug if status = -2, the loglikelihood was
   m += NR_END;    computed as likelihood omitting the logarithm. Version O.98e
   m -= nrl;  
      Revision 1.118  2006/03/14 18:20:07  brouard
      (Module): varevsij Comments added explaining the second
   /* allocate rows and set pointers to them */    table of variances if popbased=1 .
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Function pstamp added
   m[nrl] += NR_END;    (Module): Version 0.98d
   m[nrl] -= ncl;  
      Revision 1.117  2006/03/14 17:16:22  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): varevsij Comments added explaining the second
      table of variances if popbased=1 .
   /* return pointer to array of pointers to rows */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   return m;    (Module): Function pstamp added
 }    (Module): Version 0.98d
   
 /****************** free_imatrix *************************/    Revision 1.116  2006/03/06 10:29:27  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): Variance-covariance wrong links and
       int **m;    varian-covariance of ej. is needed (Saito).
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.115  2006/02/27 12:17:45  brouard
 {    (Module): One freematrix added in mlikeli! 0.98c
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.114  2006/02/26 12:57:58  brouard
 }    (Module): Some improvements in processing parameter
     filename with strsep.
 /******************* matrix *******************************/  
 double **matrix(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:
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    datafile was not closed, some imatrix were not freed and on matrix
   double **m;    allocation too.
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.112  2006/01/30 09:55:26  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   m += NR_END;  
   m -= nrl;    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Comments can be added in data file. Missing date values
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    can be a simple dot '.'.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.109  2006/01/24 19:37:15  brouard
 }    (Module): Comments (lines starting with a #) are allowed in data.
   
 /*************************free matrix ************************/    Revision 1.108  2006/01/19 18:05:42  lievre
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Gnuplot problem appeared...
 {    To be fixed
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.107  2006/01/19 16:20:37  brouard
 }    Test existence of gnuplot in imach path
   
 /******************* ma3x *******************************/    Revision 1.106  2006/01/19 13:24:36  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Some cleaning and links added in html output
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.105  2006/01/05 20:23:19  lievre
   double ***m;    *** empty log message ***
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.104  2005/09/30 16:11:43  lievre
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): sump fixed, loop imx fixed, and simplifications.
   m += NR_END;    (Module): If the status is missing at the last wave but we know
   m -= nrl;    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    contributions to the likelihood is 1 - Prob of dying from last
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   m[nrl] += NR_END;    the healthy state at last known wave). Version is 0.98
   m[nrl] -= ncl;  
     Revision 1.103  2005/09/30 15:54:49  lievre
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    (Module): sump fixed, loop imx fixed, and simplifications.
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Revision 1.102  2004/09/15 17:31:30  brouard
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Add the possibility to read data file including tab characters.
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Revision 1.101  2004/09/15 10:38:38  brouard
   for (j=ncl+1; j<=nch; j++)    Fix on curr_time
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Revision 1.100  2004/07/12 18:29:06  brouard
   for (i=nrl+1; i<=nrh; i++) {    Add version for Mac OS X. Just define UNIX in Makefile
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.99  2004/06/05 08:57:40  brouard
       m[i][j]=m[i][j-1]+nlay;    *** empty log message ***
   }  
   return m;    Revision 1.98  2004/05/16 15:05:56  brouard
 }    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 /*************************free ma3x ************************/    state at each age, but using a Gompertz model: log u =a + b*age .
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    This is the basic analysis of mortality and should be done before any
 {    other analysis, in order to test if the mortality estimated from the
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    cross-longitudinal survey is different from the mortality estimated
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    from other sources like vital statistic data.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    The same imach parameter file can be used but the option for mle should be -3.
   
 /***************** f1dim *************************/    Agnès, who wrote this part of the code, tried to keep most of the
 extern int ncom;    former routines in order to include the new code within the former code.
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    The output is very simple: only an estimate of the intercept and of
      the slope with 95% confident intervals.
 double f1dim(double x)  
 {    Current limitations:
   int j;    A) Even if you enter covariates, i.e. with the
   double f;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   double *xt;    B) There is no computation of Life Expectancy nor Life Table.
    
   xt=vector(1,ncom);    Revision 1.97  2004/02/20 13:25:42  lievre
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Version 0.96d. Population forecasting command line is (temporarily)
   f=(*nrfunc)(xt);    suppressed.
   free_vector(xt,1,ncom);  
   return f;    Revision 1.96  2003/07/15 15:38:55  brouard
 }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Revision 1.95  2003/07/08 07:54:34  brouard
 {    * imach.c (Repository):
   int iter;    (Repository): Using imachwizard code to output a more meaningful covariance
   double a,b,d,etemp;    matrix (cov(a12,c31) instead of numbers.
   double fu,fv,fw,fx;  
   double ftemp;    Revision 1.94  2003/06/27 13:00:02  brouard
   double p,q,r,tol1,tol2,u,v,w,x,xm;    Just cleaning
   double e=0.0;  
      Revision 1.93  2003/06/25 16:33:55  brouard
   a=(ax < cx ? ax : cx);    (Module): On windows (cygwin) function asctime_r doesn't
   b=(ax > cx ? ax : cx);    exist so I changed back to asctime which exists.
   x=w=v=bx;    (Module): Version 0.96b
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    Revision 1.92  2003/06/25 16:30:45  brouard
     xm=0.5*(a+b);    (Module): On windows (cygwin) function asctime_r doesn't
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    exist so I changed back to asctime which exists.
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    Revision 1.91  2003/06/25 15:30:29  brouard
 #ifdef DEBUG    * imach.c (Repository): Duplicated warning errors corrected.
     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);    (Repository): Elapsed time after each iteration is now output. It
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    helps to forecast when convergence will be reached. Elapsed time
 #endif    is stamped in powell.  We created a new html file for the graphs
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    concerning matrix of covariance. It has extension -cov.htm.
       *xmin=x;  
       return fx;    Revision 1.90  2003/06/24 12:34:15  brouard
     }    (Module): Some bugs corrected for windows. Also, when
     ftemp=fu;    mle=-1 a template is output in file "or"mypar.txt with the design
     if (fabs(e) > tol1) {    of the covariance matrix to be input.
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    Revision 1.89  2003/06/24 12:30:52  brouard
       p=(x-v)*q-(x-w)*r;    (Module): Some bugs corrected for windows. Also, when
       q=2.0*(q-r);    mle=-1 a template is output in file "or"mypar.txt with the design
       if (q > 0.0) p = -p;    of the covariance matrix to be input.
       q=fabs(q);  
       etemp=e;    Revision 1.88  2003/06/23 17:54:56  brouard
       e=d;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
       if (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 1.87  2003/06/18 12:26:01  brouard
       else {    Version 0.96
         d=p/q;  
         u=x+d;    Revision 1.86  2003/06/17 20:04:08  brouard
         if (u-a < tol2 || b-u < tol2)    (Module): Change position of html and gnuplot routines and added
           d=SIGN(tol1,xm-x);    routine fileappend.
       }  
     } else {    Revision 1.85  2003/06/17 13:12:43  brouard
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    * imach.c (Repository): Check when date of death was earlier that
     }    current date of interview. It may happen when the death was just
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    prior to the death. In this case, dh was negative and likelihood
     fu=(*f)(u);    was wrong (infinity). We still send an "Error" but patch by
     if (fu <= fx) {    assuming that the date of death was just one stepm after the
       if (u >= x) a=x; else b=x;    interview.
       SHFT(v,w,x,u)    (Repository): Because some people have very long ID (first column)
         SHFT(fv,fw,fx,fu)    we changed int to long in num[] and we added a new lvector for
         } else {    memory allocation. But we also truncated to 8 characters (left
           if (u < x) a=u; else b=u;    truncation)
           if (fu <= fw || w == x) {    (Repository): No more line truncation errors.
             v=w;  
             w=u;    Revision 1.84  2003/06/13 21:44:43  brouard
             fv=fw;    * imach.c (Repository): Replace "freqsummary" at a correct
             fw=fu;    place. It differs from routine "prevalence" which may be called
           } else if (fu <= fv || v == x || v == w) {    many times. Probs is memory consuming and must be used with
             v=u;    parcimony.
             fv=fu;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
           }  
         }    Revision 1.83  2003/06/10 13:39:11  lievre
   }    *** empty log message ***
   nrerror("Too many iterations in brent");  
   *xmin=x;    Revision 1.82  2003/06/05 15:57:20  brouard
   return fx;    Add log in  imach.c and  fullversion number is now printed.
 }  
   */
 /****************** mnbrak ***********************/  /*
      Interpolated Markov Chain
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))    Short summary of the programme:
 {    
   double ulim,u,r,q, dum;    This program computes Healthy Life Expectancies from
   double fu;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
      first survey ("cross") where individuals from different ages are
   *fa=(*func)(*ax);    interviewed on their health status or degree of disability (in the
   *fb=(*func)(*bx);    case of a health survey which is our main interest) -2- at least a
   if (*fb > *fa) {    second wave of interviews ("longitudinal") which measure each change
     SHFT(dum,*ax,*bx,dum)    (if any) in individual health status.  Health expectancies are
       SHFT(dum,*fb,*fa,dum)    computed from the time spent in each health state according to a
       }    model. More health states you consider, more time is necessary to reach the
   *cx=(*bx)+GOLD*(*bx-*ax);    Maximum Likelihood of the parameters involved in the model.  The
   *fc=(*func)(*cx);    simplest model is the multinomial logistic model where pij is the
   while (*fb > *fc) {    probability to be observed in state j at the second wave
     r=(*bx-*ax)*(*fb-*fc);    conditional to be observed in state i at the first wave. Therefore
     q=(*bx-*cx)*(*fb-*fa);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    'age' is age and 'sex' is a covariate. If you want to have a more
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    complex model than "constant and age", you should modify the program
     ulim=(*bx)+GLIMIT*(*cx-*bx);    where the markup *Covariates have to be included here again* invites
     if ((*bx-u)*(u-*cx) > 0.0) {    you to do it.  More covariates you add, slower the
       fu=(*func)(u);    convergence.
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);    The advantage of this computer programme, compared to a simple
       if (fu < *fc) {    multinomial logistic model, is clear when the delay between waves is not
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    identical for each individual. Also, if a individual missed an
           SHFT(*fb,*fc,fu,(*func)(u))    intermediate interview, the information is lost, but taken into
           }    account using an interpolation or extrapolation.  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;    hPijx is the probability to be observed in state i at age x+h
       fu=(*func)(u);    conditional to the observed state i at age x. The delay 'h' can be
     } else {    split into an exact number (nh*stepm) of unobserved intermediate
       u=(*cx)+GOLD*(*cx-*bx);    states. This elementary transition (by month, quarter,
       fu=(*func)(u);    semester or year) is modelled as a multinomial logistic.  The hPx
     }    matrix is simply the matrix product of nh*stepm elementary matrices
     SHFT(*ax,*bx,*cx,u)    and the contribution of each individual to the likelihood is simply
       SHFT(*fa,*fb,*fc,fu)    hPijx.
       }  
 }    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
 /*************** linmin ************************/    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int ncom;             Institut national d'études démographiques, Paris.
 double *pcom,*xicom;    This software have been partly granted by Euro-REVES, a concerted action
 double (*nrfunc)(double []);    from the European Union.
      It is copyrighted identically to a GNU software product, ie programme and
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    software can be distributed freely for non commercial use. Latest version
 {    can be accessed at http://euroreves.ined.fr/imach .
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   double f1dim(double x);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    
               double *fc, double (*func)(double));    **********************************************************************/
   int j;  /*
   double xx,xmin,bx,ax;    main
   double fx,fb,fa;    read parameterfile
      read datafile
   ncom=n;    concatwav
   pcom=vector(1,n);    freqsummary
   xicom=vector(1,n);    if (mle >= 1)
   nrfunc=func;      mlikeli
   for (j=1;j<=n;j++) {    print results files
     pcom[j]=p[j];    if mle==1 
     xicom[j]=xi[j];       computes hessian
   }    read end of parameter file: agemin, agemax, bage, fage, estepm
   ax=0.0;        begin-prev-date,...
   xx=1.0;    open gnuplot file
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    open html file
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 #ifdef DEBUG     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 #endif      freexexit2 possible for memory heap.
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;    h Pij x                         | pij_nom  ficrestpij
     p[j] += xi[j];     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   }         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   free_vector(xicom,1,n);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   free_vector(pcom,1,n);  
 }         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
          1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
 /*************** powell ************************/    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
             double (*func)(double []))     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
 {  
   void linmin(double p[], double xi[], int n, double *fret,    forecasting if prevfcast==1 prevforecast call prevalence()
               double (*func)(double []));    health expectancies
   int i,ibig,j;    Variance-covariance of DFLE
   double del,t,*pt,*ptt,*xit;    prevalence()
   double fp,fptt;     movingaverage()
   double *xits;    varevsij() 
   pt=vector(1,n);    if popbased==1 varevsij(,popbased)
   ptt=vector(1,n);    total life expectancies
   xit=vector(1,n);    Variance of period (stable) prevalence
   xits=vector(1,n);   end
   *fret=(*func)(p);  */
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  #define POWELL /* Instead of NLOPT */
     fp=(*fret);  /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
     ibig=0;  /* #define MNBRAKORIGINAL */ /* Don't use mnbrak fix */
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #include <math.h>
     for (i=1;i<=n;i++)  #include <stdio.h>
       printf(" %d %.12f",i, p[i]);  #include <stdlib.h>
     printf("\n");  #include <string.h>
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #ifdef _WIN32
       fptt=(*fret);  #include <io.h>
 #ifdef DEBUG  #include <windows.h>
       printf("fret=%lf \n",*fret);  #include <tchar.h>
 #endif  #else
       printf("%d",i);fflush(stdout);  #include <unistd.h>
       linmin(p,xit,n,fret,func);  #endif
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  #include <limits.h>
         ibig=i;  #include <sys/types.h>
       }  
 #ifdef DEBUG  #if defined(__GNUC__)
       printf("%d %.12e",i,(*fret));  #include <sys/utsname.h> /* Doesn't work on Windows */
       for (j=1;j<=n;j++) {  #endif
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  #include <sys/stat.h>
       }  #include <errno.h>
       for(j=1;j<=n;j++)  /* extern int errno; */
         printf(" p=%.12e",p[j]);  
       printf("\n");  /* #ifdef LINUX */
 #endif  /* #include <time.h> */
     }  /* #include "timeval.h" */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  /* #else */
 #ifdef DEBUG  /* #include <sys/time.h> */
       int k[2],l;  /* #endif */
       k[0]=1;  
       k[1]=-1;  #include <time.h>
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  #ifdef GSL
         printf(" %.12e",p[j]);  #include <gsl/gsl_errno.h>
       printf("\n");  #include <gsl/gsl_multimin.h>
       for(l=0;l<=1;l++) {  #endif
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #ifdef NLOPT
         }  #include <nlopt.h>
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  typedef struct {
       }    double (* function)(double [] );
 #endif  } myfunc_data ;
   #endif
   
       free_vector(xit,1,n);  /* #include <libintl.h> */
       free_vector(xits,1,n);  /* #define _(String) gettext (String) */
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       return;  
     }  #define GNUPLOTPROGRAM "gnuplot"
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     for (j=1;j<=n;j++) {  #define FILENAMELENGTH 132
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       pt[j]=p[j];  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     }  
     fptt=(*func)(ptt);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     if (fptt < fp) {  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  #define NINTERVMAX 8
         linmin(p,xit,n,fret,func);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
         for (j=1;j<=n;j++) {  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
           xi[j][ibig]=xi[j][n];  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
           xi[j][n]=xit[j];  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
         }  #define MAXN 20000
 #ifdef DEBUG  #define YEARM 12. /**< Number of months per year */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define AGESUP 130
         for(j=1;j<=n;j++)  #define AGEBASE 40
           printf(" %.12e",xit[j]);  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
         printf("\n");  #ifdef _WIN32
 #endif  #define DIRSEPARATOR '\\'
       }  #define CHARSEPARATOR "\\"
     }  #define ODIRSEPARATOR '/'
   }  #else
 }  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
 /**** Prevalence limit ****************/  #define ODIRSEPARATOR '\\'
   #endif
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {  /* $Id$ */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /* $State$ */
      matrix by transitions matrix until convergence is reached */  
   char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
   int i, ii,j,k;  char fullversion[]="$Revision$ $Date$"; 
   double min, max, maxmin, maxmax,sumnew=0.;  char strstart[80];
   double **matprod2();  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   double **out, cov[NCOVMAX], **pmij();  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double **newm;  int nvar=0, nforce=0; /* Number of variables, number of forces */
   double agefin, delaymax=50 ; /* Max number of years to converge */  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   for (ii=1;ii<=nlstate+ndeath;ii++)  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     for (j=1;j<=nlstate+ndeath;j++){  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     }  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   int cptcoveff=0; /* Total number of covariates to vary for printing results */
    cov[1]=1.;  int cptcov=0; /* Working variable */
    int npar=NPARMAX;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int nlstate=2; /* Number of live states */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  int ndeath=1; /* Number of dead states */
     newm=savm;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     /* Covariates have to be included here again */  int popbased=0;
      cov[2]=agefin;  
    int *wav; /* Number of waves for this individuual 0 is possible */
       for (k=1; k<=cptcovn;k++) {  int maxwav=0; /* Maxim number of waves */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       }  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       for (k=1; k<=cptcovage;k++)                     to the likelihood and the sum of weights (done by funcone)*/
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int mle=1, weightopt=0;
       for (k=1; k<=cptcovprod;k++)  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  int countcallfunc=0;  /* Count the number of calls to func */
   double jmean=1; /* Mean space between 2 waves */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  double **matprod2(); /* test */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
     savm=oldm;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     oldm=newm;  /*FILE *fic ; */ /* Used in readdata only */
     maxmax=0.;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     for(j=1;j<=nlstate;j++){  FILE *ficlog, *ficrespow;
       min=1.;  int globpr=0; /* Global variable for printing or not */
       max=0.;  double fretone; /* Only one call to likelihood */
       for(i=1; i<=nlstate; i++) {  long ipmx=0; /* Number of contributions */
         sumnew=0;  double sw; /* Sum of weights */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  char filerespow[FILENAMELENGTH];
         prlim[i][j]= newm[i][j]/(1-sumnew);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         max=FMAX(max,prlim[i][j]);  FILE *ficresilk;
         min=FMIN(min,prlim[i][j]);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       }  FILE *ficresprobmorprev;
       maxmin=max-min;  FILE *fichtm, *fichtmcov; /* Html File */
       maxmax=FMAX(maxmax,maxmin);  FILE *ficreseij;
     }  char filerese[FILENAMELENGTH];
     if(maxmax < ftolpl){  FILE *ficresstdeij;
       return prlim;  char fileresstde[FILENAMELENGTH];
     }  FILE *ficrescveij;
   }  char filerescve[FILENAMELENGTH];
 }  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 /*************** transition probabilities ***************/  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   double s1, s2;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   /*double t34;*/  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   int i,j,j1, nc, ii, jj;  char command[FILENAMELENGTH];
   int  outcmd=0;
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  char filelog[FILENAMELENGTH]; /* Log file */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char filerest[FILENAMELENGTH];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /* struct timezone tzp; */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /* extern int gettimeofday(); */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  struct tm tml, *gmtime(), *localtime();
       }  
       ps[i][j]=s2;  extern time_t time();
     }  
   }  struct tm start_time, end_time, curr_time, last_time, forecast_time;
     /*ps[3][2]=1;*/  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   struct tm tm;
   for(i=1; i<= nlstate; i++){  
      s1=0;  char strcurr[80], strfor[80];
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  char *endptr;
     for(j=i+1; j<=nlstate+ndeath; j++)  long lval;
       s1+=exp(ps[i][j]);  double dval;
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  #define NR_END 1
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #define FREE_ARG char*
     for(j=i+1; j<=nlstate+ndeath; j++)  #define FTOL 1.0e-10
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #define NRANSI 
   } /* end i */  #define ITMAX 200 
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #define TOL 2.0e-4 
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  #define CGOLD 0.3819660 
       ps[ii][ii]=1;  #define ZEPS 1.0e-10 
     }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   }  
   #define GOLD 1.618034 
   #define GLIMIT 100.0 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #define TINY 1.0e-20 
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  static double maxarg1,maxarg2;
    }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     printf("\n ");  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     }    
     printf("\n ");printf("%lf ",cov[2]);*/  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /*  #define rint(a) floor(a+0.5)
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
   goto end;*/  #define mytinydouble 1.0e-16
     return ps;  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
 }  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   /* static double dsqrarg; */
 /**************** Product of 2 matrices ******************/  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   static double sqrarg;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  int agegomp= AGEGOMP;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  int imx; 
      before: only the contents of out is modified. The function returns  int stepm=1;
      a pointer to pointers identical to out */  /* Stepm, step in month: minimum step interpolation*/
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  int estepm;
     for(k=ncolol; k<=ncoloh; k++)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  int m,nb;
   long *num;
   return out;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
   double *ageexmed,*agecens;
 /************* Higher Matrix Product ***************/  double dateintmean=0;
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double *weight;
 {  int **s; /* Status */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  double *agedc;
      duration (i.e. until  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.                    * covar=matrix(0,NCOVMAX,1,n); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
      (typically every 2 years instead of every month which is too big).  double  idx; 
      Model is determined by parameters x and covariates have to be  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
      included manually here.  int *Ndum; /** Freq of modality (tricode */
   int **codtab; /**< codtab=imatrix(1,100,1,10); */
      */  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *lsurv, *lpop, *tpop;
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double **newm;  double ftolhess; /**< Tolerance for computing hessian */
   
   /* Hstepm could be zero and should return the unit matrix */  /**************** split *************************/
   for (i=1;i<=nlstate+ndeath;i++)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[i][j]=(i==j ? 1.0 : 0.0);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       po[i][j][0]=(i==j ? 1.0 : 0.0);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     }    */ 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    char  *ss;                            /* pointer */
   for(h=1; h <=nhstepm; h++){    int   l1, l2;                         /* length counters */
     for(d=1; d <=hstepm; d++){  
       newm=savm;    l1 = strlen(path );                   /* length of path */
       /* Covariates have to be included here again */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       cov[1]=1.;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      strcpy( name, path );               /* we got the fullname name because no directory */
       for (k=1; k<=cptcovage;k++)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       for (k=1; k<=cptcovprod;k++)      /* get current working directory */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /*    extern  char* getcwd ( char *buf , int len);*/
   #ifdef WIN32
       if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  #else
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          if (getcwd(dirc, FILENAME_MAX) == NULL) {
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  #endif
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        return( GLOCK_ERROR_GETCWD );
       savm=oldm;      }
       oldm=newm;      /* got dirc from getcwd*/
     }      printf(" DIRC = %s \n",dirc);
     for(i=1; i<=nlstate+ndeath; i++)    } else {                              /* strip direcotry from path */
       for(j=1;j<=nlstate+ndeath;j++) {      ss++;                               /* after this, the filename */
         po[i][j][h]=newm[i][j];      l2 = strlen( ss );                  /* length of filename */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
          */      strcpy( name, ss );         /* save file name */
       }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   } /* end h */      dirc[l1-l2] = 0;                    /* add zero */
   return po;      printf(" DIRC2 = %s \n",dirc);
 }    }
     /* We add a separator at the end of dirc if not exists */
     l1 = strlen( dirc );                  /* length of directory */
 /*************** log-likelihood *************/    if( dirc[l1-1] != DIRSEPARATOR ){
 double func( double *x)      dirc[l1] =  DIRSEPARATOR;
 {      dirc[l1+1] = 0; 
   int i, ii, j, k, mi, d, kk;      printf(" DIRC3 = %s \n",dirc);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    }
   double **out;    ss = strrchr( name, '.' );            /* find last / */
   double sw; /* Sum of weights */    if (ss >0){
   double lli; /* Individual log likelihood */      ss++;
   long ipmx;      strcpy(ext,ss);                     /* save extension */
   /*extern weight */      l1= strlen( name);
   /* We are differentiating ll according to initial status */      l2= strlen(ss)+1;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      strncpy( finame, name, l1-l2);
   /*for(i=1;i<imx;i++)      finame[l1-l2]= 0;
     printf(" %d\n",s[4][i]);    }
   */  
   cov[1]=1.;    return( 0 );                          /* we're done */
   }
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /******************************************/
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  void replace_back_to_slash(char *s, char*t)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
       for(d=0; d<dh[mi][i]; d++){    int i;
         newm=savm;    int lg=0;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    i=0;
         for (kk=1; kk<=cptcovage;kk++) {    lg=strlen(t);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    for(i=0; i<= lg; i++) {
         }      (s[i] = t[i]);
              if (t[i]== '\\') s[i]='/';
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  }
         savm=oldm;  
         oldm=newm;  char *trimbb(char *out, char *in)
          { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
            char *s;
       } /* end mult */    s=out;
          while (*in != '\0'){
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        in++;
       ipmx +=1;      }
       sw += weight[i];      *out++ = *in++;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    }
     } /* end of wave */    *out='\0';
   } /* end of individual */    return s;
   }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  char *cutl(char *blocc, char *alocc, char *in, char occ)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  {
   return -l;    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
 }       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns blocc
 /*********** Maximum Likelihood Estimation ***************/    */
     char *s, *t;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    t=in;s=in;
 {    while ((*in != occ) && (*in != '\0')){
   int i,j, iter;      *alocc++ = *in++;
   double **xi,*delti;    }
   double fret;    if( *in == occ){
   xi=matrix(1,npar,1,npar);      *(alocc)='\0';
   for (i=1;i<=npar;i++)      s=++in;
     for (j=1;j<=npar;j++)    }
       xi[i][j]=(i==j ? 1.0 : 0.0);   
   printf("Powell\n");    if (s == t) {/* occ not found */
   powell(p,xi,npar,ftol,&iter,&fret,func);      *(alocc-(in-s))='\0';
       in=s;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    while ( *in != '\0'){
       *blocc++ = *in++;
 }    }
   
 /**** Computes Hessian and covariance matrix ***/    *blocc='\0';
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    return t;
 {  }
   double  **a,**y,*x,pd;  char *cutv(char *blocc, char *alocc, char *in, char occ)
   double **hess;  {
   int i, j,jk;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   int *indx;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
   double hessii(double p[], double delta, int theta, double delti[]);       If occ is not found blocc is null and alocc is equal to in. Returns alocc
   double hessij(double p[], double delti[], int i, int j);    */
   void lubksb(double **a, int npar, int *indx, double b[]) ;    char *s, *t;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    t=in;s=in;
     while (*in != '\0'){
   hess=matrix(1,npar,1,npar);      while( *in == occ){
         *blocc++ = *in++;
   printf("\nCalculation of the hessian matrix. Wait...\n");        s=in;
   for (i=1;i<=npar;i++){      }
     printf("%d",i);fflush(stdout);      *blocc++ = *in++;
     hess[i][i]=hessii(p,ftolhess,i,delti);    }
     /*printf(" %f ",p[i]);*/    if (s == t) /* occ not found */
     /*printf(" %lf ",hess[i][i]);*/      *(blocc-(in-s))='\0';
   }    else
        *(blocc-(in-s)-1)='\0';
   for (i=1;i<=npar;i++) {    in=s;
     for (j=1;j<=npar;j++)  {    while ( *in != '\0'){
       if (j>i) {      *alocc++ = *in++;
         printf(".%d%d",i,j);fflush(stdout);    }
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];        *alocc='\0';
         /*printf(" %lf ",hess[i][j]);*/    return s;
       }  }
     }  
   }  int nbocc(char *s, char occ)
   printf("\n");  {
     int i,j=0;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    int lg=20;
      i=0;
   a=matrix(1,npar,1,npar);    lg=strlen(s);
   y=matrix(1,npar,1,npar);    for(i=0; i<= lg; i++) {
   x=vector(1,npar);    if  (s[i] == occ ) j++;
   indx=ivector(1,npar);    }
   for (i=1;i<=npar;i++)    return j;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /* void cutv(char *u,char *v, char*t, char occ) */
   for (j=1;j<=npar;j++) {  /* { */
     for (i=1;i<=npar;i++) x[i]=0;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     x[j]=1;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     lubksb(a,npar,indx,x);  /*      gives u="abcdef2ghi" and v="j" *\/ */
     for (i=1;i<=npar;i++){  /*   int i,lg,j,p=0; */
       matcov[i][j]=x[i];  /*   i=0; */
     }  /*   lg=strlen(t); */
   }  /*   for(j=0; j<=lg-1; j++) { */
   /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   printf("\n#Hessian matrix#\n");  /*   } */
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++) {  /*   for(j=0; j<p; j++) { */
       printf("%.3e ",hess[i][j]);  /*     (u[j] = t[j]); */
     }  /*   } */
     printf("\n");  /*      u[p]='\0'; */
   }  
   /*    for(j=0; j<= lg; j++) { */
   /* Recompute Inverse */  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   for (i=1;i<=npar;i++)  /*   } */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /* } */
   ludcmp(a,npar,indx,&pd);  
   #ifdef _WIN32
   /*  printf("\n#Hessian matrix recomputed#\n");  char * strsep(char **pp, const char *delim)
   {
   for (j=1;j<=npar;j++) {    char *p, *q;
     for (i=1;i<=npar;i++) x[i]=0;           
     x[j]=1;    if ((p = *pp) == NULL)
     lubksb(a,npar,indx,x);      return 0;
     for (i=1;i<=npar;i++){    if ((q = strpbrk (p, delim)) != NULL)
       y[i][j]=x[i];    {
       printf("%.3e ",y[i][j]);      *pp = q + 1;
     }      *q = '\0';
     printf("\n");    }
   }    else
   */      *pp = 0;
     return p;
   free_matrix(a,1,npar,1,npar);  }
   free_matrix(y,1,npar,1,npar);  #endif
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);  /********************** nrerror ********************/
   free_matrix(hess,1,npar,1,npar);  
   void nrerror(char error_text[])
   {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /*************** hessian matrix ****************/    exit(EXIT_FAILURE);
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  /*********************** vector *******************/
   int i;  double *vector(int nl, int nh)
   int l=1, lmax=20;  {
   double k1,k2;    double *v;
   double p2[NPARMAX+1];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double res;    if (!v) nrerror("allocation failure in vector");
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    return v-nl+NR_END;
   double fx;  }
   int k=0,kmax=10;  
   double l1;  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
   fx=func(x);  {
   for (i=1;i<=npar;i++) p2[i]=x[i];    free((FREE_ARG)(v+nl-NR_END));
   for(l=0 ; l <=lmax; l++){  }
     l1=pow(10,l);  
     delts=delt;  /************************ivector *******************************/
     for(k=1 ; k <kmax; k=k+1){  int *ivector(long nl,long nh)
       delt = delta*(l1*k);  {
       p2[theta]=x[theta] +delt;    int *v;
       k1=func(p2)-fx;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       p2[theta]=x[theta]-delt;    if (!v) nrerror("allocation failure in ivector");
       k2=func(p2)-fx;    return v-nl+NR_END;
       /*res= (k1-2.0*fx+k2)/delt/delt; */  }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
        /******************free ivector **************************/
 #ifdef DEBUG  void free_ivector(int *v, long nl, long nh)
       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);  {
 #endif    free((FREE_ARG)(v+nl-NR_END));
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;  /************************lvector *******************************/
       }  long *lvector(long nl,long nh)
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  {
         k=kmax; l=lmax*10.;    long *v;
       }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    if (!v) nrerror("allocation failure in ivector");
         delts=delt;    return v-nl+NR_END;
       }  }
     }  
   }  /******************free lvector **************************/
   delti[theta]=delts;  void free_lvector(long *v, long nl, long nh)
   return res;  {
      free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  /******************* imatrix *******************************/
 {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   int i;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   int l=1, l1, lmax=20;  { 
   double k1,k2,k3,k4,res,fx;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double p2[NPARMAX+1];    int **m; 
   int k;    
     /* allocate pointers to rows */ 
   fx=func(x);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   for (k=1; k<=2; k++) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
     for (i=1;i<=npar;i++) p2[i]=x[i];    m += NR_END; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    m -= nrl; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    
     k1=func(p2)-fx;    
      /* allocate rows and set pointers to them */ 
     p2[thetai]=x[thetai]+delti[thetai]/k;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     k2=func(p2)-fx;    m[nrl] += NR_END; 
      m[nrl] -= ncl; 
     p2[thetai]=x[thetai]-delti[thetai]/k;    
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     k3=func(p2)-fx;    
      /* return pointer to array of pointers to rows */ 
     p2[thetai]=x[thetai]-delti[thetai]/k;    return m; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  } 
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  /****************** free_imatrix *************************/
 #ifdef DEBUG  void free_imatrix(m,nrl,nrh,ncl,nch)
     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);        int **m;
 #endif        long nch,ncl,nrh,nrl; 
   }       /* free an int matrix allocated by imatrix() */ 
   return res;  { 
 }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
 /************** Inverse of matrix **************/  } 
 void ludcmp(double **a, int n, int *indx, double *d)  
 {  /******************* matrix *******************************/
   int i,imax,j,k;  double **matrix(long nrl, long nrh, long ncl, long nch)
   double big,dum,sum,temp;  {
   double *vv;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      double **m;
   vv=vector(1,n);  
   *d=1.0;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (i=1;i<=n;i++) {    if (!m) nrerror("allocation failure 1 in matrix()");
     big=0.0;    m += NR_END;
     for (j=1;j<=n;j++)    m -= nrl;
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     vv[i]=1.0/big;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   }    m[nrl] += NR_END;
   for (j=1;j<=n;j++) {    m[nrl] -= ncl;
     for (i=1;i<j;i++) {  
       sum=a[i][j];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    return m;
       a[i][j]=sum;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     }  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     big=0.0;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     for (i=j;i<=n;i++) {     */
       sum=a[i][j];  }
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  /*************************free matrix ************************/
       a[i][j]=sum;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       if ( (dum=vv[i]*fabs(sum)) >= big) {  {
         big=dum;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         imax=i;    free((FREE_ARG)(m+nrl-NR_END));
       }  }
     }  
     if (j != imax) {  /******************* ma3x *******************************/
       for (k=1;k<=n;k++) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         dum=a[imax][k];  {
         a[imax][k]=a[j][k];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         a[j][k]=dum;    double ***m;
       }  
       *d = -(*d);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       vv[imax]=vv[j];    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     indx[j]=imax;    m -= nrl;
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       dum=1.0/(a[j][j]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    m[nrl] += NR_END;
     }    m[nrl] -= ncl;
   }  
   free_vector(vv,1,n);  /* Doesn't work */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 ;  
 }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 void lubksb(double **a, int n, int *indx, double b[])    m[nrl][ncl] += NR_END;
 {    m[nrl][ncl] -= nll;
   int i,ii=0,ip,j;    for (j=ncl+1; j<=nch; j++) 
   double sum;      m[nrl][j]=m[nrl][j-1]+nlay;
      
   for (i=1;i<=n;i++) {    for (i=nrl+1; i<=nrh; i++) {
     ip=indx[i];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     sum=b[ip];      for (j=ncl+1; j<=nch; j++) 
     b[ip]=b[i];        m[i][j]=m[i][j-1]+nlay;
     if (ii)    }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    return m; 
     else if (sum) ii=i;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     b[i]=sum;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   }    */
   for (i=n;i>=1;i--) {  }
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*************************free ma3x ************************/
     b[i]=sum/a[i][i];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   }  {
 }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 /************ Frequencies ********************/    free((FREE_ARG)(m+nrl-NR_END));
 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)  }
 {  /* Some frequencies */  
    /*************** function subdirf ***********/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  char *subdirf(char fileres[])
   double ***freq; /* Frequencies */  {
   double *pp;    /* Caution optionfilefiname is hidden */
   double pos, k2, dateintsum=0,k2cpt=0;    strcpy(tmpout,optionfilefiname);
   FILE *ficresp;    strcat(tmpout,"/"); /* Add to the right */
   char fileresp[FILENAMELENGTH];    strcat(tmpout,fileres);
     return tmpout;
   pp=vector(1,nlstate);  }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");  /*************** function subdirf2 ***********/
   strcat(fileresp,fileres);  char *subdirf2(char fileres[], char *preop)
   if((ficresp=fopen(fileresp,"w"))==NULL) {  {
     printf("Problem with prevalence resultfile: %s\n", fileresp);    
     exit(0);    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    strcat(tmpout,"/");
   j1=0;    strcat(tmpout,preop);
     strcat(tmpout,fileres);
   j=cptcoveff;    return tmpout;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
   
   for(k1=1; k1<=j;k1++){  /*************** function subdirf3 ***********/
    for(i1=1; i1<=ncodemax[k1];i1++){  char *subdirf3(char fileres[], char *preop, char *preop2)
        j1++;  {
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    
          scanf("%d", i);*/    /* Caution optionfilefiname is hidden */
         for (i=-1; i<=nlstate+ndeath; i++)      strcpy(tmpout,optionfilefiname);
          for (jk=-1; jk<=nlstate+ndeath; jk++)      strcat(tmpout,"/");
            for(m=agemin; m <= agemax+3; m++)    strcat(tmpout,preop);
              freq[i][jk][m]=0;    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
         dateintsum=0;    return tmpout;
         k2cpt=0;  }
        for (i=1; i<=imx; i++) {  
          bool=1;  char *asc_diff_time(long time_sec, char ascdiff[])
          if  (cptcovn>0) {  {
            for (z1=1; z1<=cptcoveff; z1++)    long sec_left, days, hours, minutes;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    days = (time_sec) / (60*60*24);
                bool=0;    sec_left = (time_sec) % (60*60*24);
          }    hours = (sec_left) / (60*60) ;
          if (bool==1) {    sec_left = (sec_left) %(60*60);
            for(m=firstpass; m<=lastpass; m++){    minutes = (sec_left) /60;
              k2=anint[m][i]+(mint[m][i]/12.);    sec_left = (sec_left) % (60);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
                if(agev[m][i]==0) agev[m][i]=agemax+1;    return ascdiff;
                if(agev[m][i]==1) agev[m][i]=agemax+2;  }
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  /***************** f1dim *************************/
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  extern int ncom; 
                  dateintsum=dateintsum+k2;  extern double *pcom,*xicom;
                  k2cpt++;  extern double (*nrfunc)(double []); 
                }   
   double f1dim(double x) 
              }  { 
            }    int j; 
          }    double f;
        }    double *xt; 
         if  (cptcovn>0) {   
          fprintf(ficresp, "\n#********** Variable ");    xt=vector(1,ncom); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
        fprintf(ficresp, "**********\n#");    f=(*nrfunc)(xt); 
         }    free_vector(xt,1,ncom); 
        for(i=1; i<=nlstate;i++)    return f; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  } 
        fprintf(ficresp, "\n");  
          /*****************brent *************************/
   for(i=(int)agemin; i <= (int)agemax+3; i++){  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     if(i==(int)agemax+3)  { 
       printf("Total");    int iter; 
     else    double a,b,d,etemp;
       printf("Age %d", i);    double fu=0,fv,fw,fx;
     for(jk=1; jk <=nlstate ; jk++){    double ftemp=0.;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         pp[jk] += freq[jk][m][i];    double e=0.0; 
     }   
     for(jk=1; jk <=nlstate ; jk++){    a=(ax < cx ? ax : cx); 
       for(m=-1, pos=0; m <=0 ; m++)    b=(ax > cx ? ax : cx); 
         pos += freq[jk][m][i];    x=w=v=bx; 
       if(pp[jk]>=1.e-10)    fw=fv=fx=(*f)(x); 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    for (iter=1;iter<=ITMAX;iter++) { 
       else      xm=0.5*(a+b); 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
      for(jk=1; jk <=nlstate ; jk++){      fprintf(ficlog,".");fflush(ficlog);
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  #ifdef DEBUGBRENT
         pp[jk] += freq[jk][m][i];      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
      }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(jk=1,pos=0; jk <=nlstate ; jk++)  #endif
       pos += pp[jk];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     for(jk=1; jk <=nlstate ; jk++){        *xmin=x; 
       if(pos>=1.e-5)        return fx; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      } 
       else      ftemp=fu;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      if (fabs(e) > tol1) { 
       if( i <= (int) agemax){        r=(x-w)*(fx-fv); 
         if(pos>=1.e-5){        q=(x-v)*(fx-fw); 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        p=(x-v)*q-(x-w)*r; 
           probs[i][jk][j1]= pp[jk]/pos;        q=2.0*(q-r); 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        if (q > 0.0) p = -p; 
         }        q=fabs(q); 
       else        etemp=e; 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        e=d; 
       }        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)); 
     for(jk=-1; jk <=nlstate+ndeath; jk++)        else { 
       for(m=-1; m <=nlstate+ndeath; m++)          d=p/q; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          u=x+d; 
     if(i <= (int) agemax)          if (u-a < tol2 || b-u < tol2) 
       fprintf(ficresp,"\n");            d=SIGN(tol1,xm-x); 
     printf("\n");        } 
     }      } else { 
     }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
  }      } 
   dateintmean=dateintsum/k2cpt;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        fu=(*f)(u); 
   fclose(ficresp);      if (fu <= fx) { 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        if (u >= x) a=x; else b=x; 
   free_vector(pp,1,nlstate);        SHFT(v,w,x,u) 
         SHFT(fv,fw,fx,fu) 
   /* End of Freq */      } else { 
 }        if (u < x) a=u; else b=u; 
         if (fu <= fw || w == x) { 
 /************ Prevalence ********************/          v=w; 
 void prevalence(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 calagedate)          w=u; 
 {  /* Some frequencies */          fv=fw; 
            fw=fu; 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        } else if (fu <= fv || v == x || v == w) { 
   double ***freq; /* Frequencies */          v=u; 
   double *pp;          fv=fu; 
   double pos, k2;        } 
       } 
   pp=vector(1,nlstate);    } 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    nrerror("Too many iterations in brent"); 
      *xmin=x; 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    return fx; 
   j1=0;  } 
    
   j=cptcoveff;  /****************** mnbrak ***********************/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
  for(k1=1; k1<=j;k1++){              double (*func)(double)) 
     for(i1=1; i1<=ncodemax[k1];i1++){  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
       j1++;  the downhill direction (defined by the function as evaluated at the initial points) and returns
    new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
       for (i=-1; i<=nlstate+ndeath; i++)    values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
         for (jk=-1; jk<=nlstate+ndeath; jk++)       */
           for(m=agemin; m <= agemax+3; m++)    double ulim,u,r,q, dum;
             freq[i][jk][m]=0;    double fu; 
         
       for (i=1; i<=imx; i++) {    *fa=(*func)(*ax); 
         bool=1;    *fb=(*func)(*bx); 
         if  (cptcovn>0) {    if (*fb > *fa) { 
           for (z1=1; z1<=cptcoveff; z1++)      SHFT(dum,*ax,*bx,dum) 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      SHFT(dum,*fb,*fa,dum) 
               bool=0;    } 
         }    *cx=(*bx)+GOLD*(*bx-*ax); 
         if (bool==1) {    *fc=(*func)(*cx); 
           for(m=firstpass; m<=lastpass; m++){  #ifdef DEBUG
             k2=anint[m][i]+(mint[m][i]/12.);    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
               if(agev[m][i]==0) agev[m][i]=agemax+1;  #endif
               if(agev[m][i]==1) agev[m][i]=agemax+2;    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      r=(*bx-*ax)*(*fb-*fc); 
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];        q=(*bx-*cx)*(*fb-*fa); 
             }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
           }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
         }      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=(int)agemin; i <= (int)agemax+3; i++){  #ifdef DEBUG
           for(jk=1; jk <=nlstate ; jk++){        /* f(x)=A(x-u)**2+f(u) */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        double A, fparabu; 
               pp[jk] += freq[jk][m][i];        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
           }        fparabu= *fa - A*(*ax-u)*(*ax-u);
           for(jk=1; jk <=nlstate ; jk++){        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);
             for(m=-1, pos=0; m <=0 ; m++)        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);
             pos += freq[jk][m][i];        /* And thus,it can be that fu > *fc even if fparabu < *fc */
         }        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
                  (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
          for(jk=1; jk <=nlstate ; jk++){        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  #endif 
              pp[jk] += freq[jk][m][i];  #ifdef MNBRAKORIGINAL
          }  #else
                  if (fu > *fc) {
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  #ifdef DEBUG
         printf("mnbrak4  fu > fc \n");
          for(jk=1; jk <=nlstate ; jk++){                  fprintf(ficlog, "mnbrak4 fu > fc\n");
            if( i <= (int) agemax){  #endif
              if(pos>=1.e-5){          /* 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 *\/  */
                probs[i][jk][j1]= pp[jk]/pos;          /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
              }          dum=u; /* Shifting c and u */
            }          u = *cx;
          }          *cx = dum;
                    dum = fu;
         }          fu = *fc;
     }          *fc =dum;
   }        } else { /* end */
    #ifdef DEBUG
          printf("mnbrak3  fu < fc \n");
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        fprintf(ficlog, "mnbrak3 fu < fc\n");
   free_vector(pp,1,nlstate);  #endif
            dum=u; /* Shifting c and u */
 }  /* End of Freq */          u = *cx;
           *cx = dum;
 /************* Waves Concatenation ***************/          dum = fu;
           fu = *fc;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          *fc =dum;
 {        }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  #endif
      Death is a valid wave (if date is known).      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  #ifdef DEBUG
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        printf("mnbrak2  u after c but before ulim\n");
      and mw[mi+1][i]. dh depends on stepm.        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
      */  #endif
         fu=(*func)(u); 
   int i, mi, m;        if (fu < *fc) { 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  #ifdef DEBUG
      double sum=0., jmean=0.;*/        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
         fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
   int j, k=0,jk, ju, jl;  #endif
   double sum=0.;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   jmin=1e+5;          SHFT(*fb,*fc,fu,(*func)(u)) 
   jmax=-1;        } 
   jmean=0.;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   for(i=1; i<=imx; i++){  #ifdef DEBUG
     mi=0;        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
     m=firstpass;        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
     while(s[m][i] <= nlstate){  #endif
       if(s[m][i]>=1)        u=ulim; 
         mw[++mi][i]=m;        fu=(*func)(u); 
       if(m >=lastpass)      } else { /* u could be left to b (if r > q parabola has a maximum) */
         break;  #ifdef DEBUG
       else        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
         m++;        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
     }/* end while */  #endif
     if (s[m][i] > nlstate){        u=(*cx)+GOLD*(*cx-*bx); 
       mi++;     /* Death is another wave */        fu=(*func)(u); 
       /* if(mi==0)  never been interviewed correctly before death */      } /* end tests */
          /* Only death is a correct wave */      SHFT(*ax,*bx,*cx,u) 
       mw[mi][i]=m;      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);
     wav[i]=mi;        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);
     if(mi==0)  #endif
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    } /* 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<=imx; i++){  /*************** linmin ************************/
     for(mi=1; mi<wav[i];mi++){  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
       if (stepm <=0)  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
         dh[mi][i]=1;  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
       else{  the value of func at the returned location p . This is actually all accomplished by calling the
         if (s[mw[mi+1][i]][i] > nlstate) {  routines mnbrak and brent .*/
           if (agedc[i] < 2*AGESUP) {  int ncom; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  double *pcom,*xicom;
           if(j==0) j=1;  /* Survives at least one month after exam */  double (*nrfunc)(double []); 
           k=k+1;   
           if (j >= jmax) jmax=j;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           if (j <= jmin) jmin=j;  { 
           sum=sum+j;    double brent(double ax, double bx, double cx, 
           /* if (j<10) printf("j=%d num=%d ",j,i); */                 double (*f)(double), double tol, double *xmin); 
           }    double f1dim(double x); 
         }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         else{                double *fc, double (*func)(double)); 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    int j; 
           k=k+1;    double xx,xmin,bx,ax; 
           if (j >= jmax) jmax=j;    double fx,fb,fa;
           else if (j <= jmin)jmin=j;   
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    ncom=n; 
           sum=sum+j;    pcom=vector(1,n); 
         }    xicom=vector(1,n); 
         jk= j/stepm;    nrfunc=func; 
         jl= j -jk*stepm;    for (j=1;j<=n;j++) { 
         ju= j -(jk+1)*stepm;      pcom[j]=p[j]; 
         if(jl <= -ju)      xicom[j]=xi[j]; 
           dh[mi][i]=jk;    } 
         else    ax=0.0; 
           dh[mi][i]=jk+1;    xx=1.0; 
         if(dh[mi][i]==0)    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
           dh[mi][i]=1; /* At least one step */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
       }  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   jmean=sum/k;  #endif
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    for (j=1;j<=n;j++) { 
  }      xi[j] *= xmin; 
 /*********** Tricode ****************************/      p[j] += xi[j]; 
 void tricode(int *Tvar, int **nbcode, int imx)    } 
 {    free_vector(xicom,1,n); 
   int Ndum[20],ij=1, k, j, i;    free_vector(pcom,1,n); 
   int cptcode=0;  } 
   cptcoveff=0;  
    
   for (k=0; k<19; k++) Ndum[k]=0;  /*************** powell ************************/
   for (k=1; k<=7; k++) ncodemax[k]=0;  /*
   Minimization of a function func of n variables. Input consists of an initial starting point
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
     for (i=1; i<=imx; i++) {  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
       ij=(int)(covar[Tvar[j]][i]);  such that failure to decrease by more than this amount on one iteration signals doneness. On
       Ndum[ij]++;  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  function value at p , and iter is the number of iterations taken. The routine linmin is used.
       if (ij > cptcode) cptcode=ij;   */
     }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
     for (i=0; i<=cptcode; i++) {  { 
       if(Ndum[i]!=0) ncodemax[j]++;    void linmin(double p[], double xi[], int n, double *fret, 
     }                double (*func)(double [])); 
     ij=1;    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
     double directest;
     for (i=1; i<=ncodemax[j]; i++) {    double fp,fptt;
       for (k=0; k<=19; k++) {    double *xits;
         if (Ndum[k] != 0) {    int niterf, itmp;
           nbcode[Tvar[j]][ij]=k;  
           ij++;    pt=vector(1,n); 
         }    ptt=vector(1,n); 
         if (ij > ncodemax[j]) break;    xit=vector(1,n); 
       }      xits=vector(1,n); 
     }    *fret=(*func)(p); 
   }      for (j=1;j<=n;j++) pt[j]=p[j]; 
       rcurr_time = time(NULL);  
  for (k=0; k<19; k++) Ndum[k]=0;    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
  for (i=1; i<=ncovmodel-2; i++) {      ibig=0; 
       ij=Tvar[i];      del=0.0; 
       Ndum[ij]++;      rlast_time=rcurr_time;
     }      /* (void) gettimeofday(&curr_time,&tzp); */
       rcurr_time = time(NULL);  
  ij=1;      curr_time = *localtime(&rcurr_time);
  for (i=1; i<=10; i++) {      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
    if((Ndum[i]!=0) && (i<=ncov)){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
      Tvaraff[ij]=i;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
      ij++;     for (i=1;i<=n;i++) {
    }        printf(" %d %.12f",i, p[i]);
  }        fprintf(ficlog," %d %.12lf",i, p[i]);
          fprintf(ficrespow," %.12lf", p[i]);
     cptcoveff=ij-1;      }
 }      printf("\n");
       fprintf(ficlog,"\n");
 /*********** Health Expectancies ****************/      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        tml = *localtime(&rcurr_time);
 {        strcpy(strcurr,asctime(&tml));
   /* Health expectancies */        rforecast_time=rcurr_time; 
   int i, j, nhstepm, hstepm, h;        itmp = strlen(strcurr);
   double age, agelim,hf;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double ***p3mat;          strcurr[itmp-1]='\0';
          printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   fprintf(ficreseij,"# Health expectancies\n");        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   fprintf(ficreseij,"# Age");        for(niterf=10;niterf<=30;niterf+=10){
   for(i=1; i<=nlstate;i++)          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
     for(j=1; j<=nlstate;j++)          forecast_time = *localtime(&rforecast_time);
       fprintf(ficreseij," %1d-%1d",i,j);          strcpy(strfor,asctime(&forecast_time));
   fprintf(ficreseij,"\n");          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   hstepm=1*YEARM; /*  Every j years of age (in month) */          strfor[itmp-1]='\0';
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          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);
           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);
   agelim=AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     /* nhstepm age range expressed in number of stepm */      for (i=1;i<=n;i++) { 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     /* Typically if 20 years = 20*12/6=40 stepm */        fptt=(*fret); 
     if (stepm >= YEARM) hstepm=1;  #ifdef DEBUG
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  #endif
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        printf("%d",i);fflush(stdout);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
         if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
     for(i=1; i<=nlstate;i++)                                         because that direction will be replaced unless the gain del is small
       for(j=1; j<=nlstate;j++)                                        in comparison with the 'probable' gain, mu^2, with the last average direction.
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){                                        Unless the n directions are conjugate some gain in the determinant may be obtained
           eij[i][j][(int)age] +=p3mat[i][j][h];                                        with the new direction.
         }                                        */
              del=fabs(fptt-(*fret)); 
     hf=1;          ibig=i; 
     if (stepm >= YEARM) hf=stepm/YEARM;        } 
     fprintf(ficreseij,"%.0f",age );  #ifdef DEBUG
     for(i=1; i<=nlstate;i++)        printf("%d %.12e",i,(*fret));
       for(j=1; j<=nlstate;j++){        fprintf(ficlog,"%d %.12e",i,(*fret));
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        for (j=1;j<=n;j++) {
       }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     fprintf(ficreseij,"\n");          printf(" x(%d)=%.12e",j,xit[j]);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   }        }
 }        for(j=1;j<=n;j++) {
           printf(" p(%d)=%.12e",j,p[j]);
 /************ Variance ******************/          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
 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)        }
 {        printf("\n");
   /* Variance of health expectancies */        fprintf(ficlog,"\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  #endif
   double **newm;      } /* end i */
   double **dnewm,**doldm;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
   int i, j, nhstepm, hstepm, h;  #ifdef DEBUG
   int k, cptcode;        int k[2],l;
   double *xp;        k[0]=1;
   double **gp, **gm;        k[1]=-1;
   double ***gradg, ***trgradg;        printf("Max: %.12e",(*func)(p));
   double ***p3mat;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double age,agelim;        for (j=1;j<=n;j++) {
   int theta;          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
    fprintf(ficresvij,"# Covariances of life expectancies\n");        }
   fprintf(ficresvij,"# Age");        printf("\n");
   for(i=1; i<=nlstate;i++)        fprintf(ficlog,"\n");
     for(j=1; j<=nlstate;j++)        for(l=0;l<=1;l++) {
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          for (j=1;j<=n;j++) {
   fprintf(ficresvij,"\n");            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   xp=vector(1,npar);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   dnewm=matrix(1,nlstate,1,npar);          }
   doldm=matrix(1,nlstate,1,nlstate);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
            fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   hstepm=1*YEARM; /* Every year of age */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  #endif
   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 */        free_vector(xit,1,n); 
     if (stepm >= YEARM) hstepm=1;        free_vector(xits,1,n); 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        free_vector(ptt,1,n); 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        free_vector(pt,1,n); 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        return; 
     gp=matrix(0,nhstepm,1,nlstate);      } 
     gm=matrix(0,nhstepm,1,nlstate);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
     for(theta=1; theta <=npar; theta++){        ptt[j]=2.0*p[j]-pt[j]; 
       for(i=1; i<=npar; i++){ /* Computes gradient */        xit[j]=p[j]-pt[j]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        pt[j]=p[j]; 
       }      } 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fptt=(*func)(ptt); /* f_3 */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
         /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       if (popbased==1) {        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         for(i=1; i<=nlstate;i++)        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
           prlim[i][i]=probs[(int)age][i][ij];        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
       }        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
              /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
       for(j=1; j<= nlstate; j++){        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
         for(h=0; h<=nhstepm; h++){  #ifdef NRCORIGINAL
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  #else
         }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       }        t= t- del*SQR(fp-fptt);
      #endif
       for(i=1; i<=npar; i++) /* Computes gradient */        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  #ifdef DEBUG
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          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);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        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),
       if (popbased==1) {               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         for(i=1; i<=nlstate;i++)        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
           prlim[i][i]=probs[(int)age][i][ij];               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
       }        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
         fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
       for(j=1; j<= nlstate; j++){  #endif
         for(h=0; h<=nhstepm; h++){  #ifdef POWELLORIGINAL
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        if (t < 0.0) { /* Then we use it for new direction */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  #else
         }        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);
         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       for(j=1; j<= nlstate; j++)        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
         for(h=0; h<=nhstepm; h++){        fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      } 
         }        if (directest < 0.0) { /* Then we use it for new direction */
     } /* End theta */  #endif
           linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
     for(h=0; h<=nhstepm; h++)            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
       for(j=1; j<=nlstate;j++)          }
         for(theta=1; theta <=npar; theta++)          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
           trgradg[h][j][theta]=gradg[h][theta][j];          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
       for(j=1;j<=nlstate;j++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         vareij[i][j][(int)age] =0.;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(h=0;h<=nhstepm;h++){          for(j=1;j<=n;j++){
       for(k=0;k<=nhstepm;k++){            printf(" %.12e",xit[j]);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);            fprintf(ficlog," %.12e",xit[j]);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          }
         for(i=1;i<=nlstate;i++)          printf("\n");
           for(j=1;j<=nlstate;j++)          fprintf(ficlog,"\n");
             vareij[i][j][(int)age] += doldm[i][j];  #endif
       }        } /* end of t negative */
     }      } /* end if (fptt < fp)  */
     h=1;    } 
     if (stepm >= YEARM) h=stepm/YEARM;  } 
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  /**** Prevalence limit (stable or period prevalence)  ****************/
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       }  {
     fprintf(ficresvij,"\n");    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     free_matrix(gp,0,nhstepm,1,nlstate);       matrix by transitions matrix until convergence is reached */
     free_matrix(gm,0,nhstepm,1,nlstate);    
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    int i, ii,j,k;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double min, max, maxmin, maxmax,sumnew=0.;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* 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 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)    cov[1]=1.;
 {    
   /* Variance of prevalence limit */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double **newm;      newm=savm;
   double **dnewm,**doldm;      /* Covariates have to be included here again */
   int i, j, nhstepm, hstepm;      cov[2]=agefin;
   int k, cptcode;      
   double *xp;      for (k=1; k<=cptcovn;k++) {
   double *gp, *gm;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double **gradg, **trgradg;        /*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]]);*/
   double age,agelim;      }
   int theta;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
          /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   fprintf(ficresvpl,"# Age");      
   for(i=1; i<=nlstate;i++)      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       fprintf(ficresvpl," %1d-%1d",i,i);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   fprintf(ficresvpl,"\n");      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   xp=vector(1,npar);      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   dnewm=matrix(1,nlstate,1,npar);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   doldm=matrix(1,nlstate,1,nlstate);      
        savm=oldm;
   hstepm=1*YEARM; /* Every year of age */      oldm=newm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      maxmax=0.;
   agelim = AGESUP;      for(j=1;j<=nlstate;j++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        min=1.;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        max=0.;
     if (stepm >= YEARM) hstepm=1;        for(i=1; i<=nlstate; i++) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          sumnew=0;
     gradg=matrix(1,npar,1,nlstate);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     gp=vector(1,nlstate);          prlim[i][j]= newm[i][j]/(1-sumnew);
     gm=vector(1,nlstate);          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           max=FMAX(max,prlim[i][j]);
     for(theta=1; theta <=npar; theta++){          min=FMIN(min,prlim[i][j]);
       for(i=1; i<=npar; i++){ /* Computes gradient */        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        maxmin=max-min;
       }        maxmax=FMAX(maxmax,maxmin);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } /* j loop */
       for(i=1;i<=nlstate;i++)      if(maxmax < ftolpl){
         gp[i] = prlim[i][i];        return prlim;
          }
       for(i=1; i<=npar; i++) /* Computes gradient */    } /* age loop */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    return prlim; /* should not reach here */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];  /*************** transition probabilities ***************/ 
   
       for(i=1;i<=nlstate;i++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  {
     } /* End theta */    /* According to parameters values stored in x and the covariate's values stored in cov,
        computes the probability to be observed in state j being in state i by appying the
     trgradg =matrix(1,nlstate,1,npar);       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]
     for(j=1; j<=nlstate;j++)       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
       for(theta=1; theta <=npar; theta++)       ncth covariate in the global vector x is given by the formula:
         trgradg[j][theta]=gradg[theta][j];       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     for(i=1;i<=nlstate;i++)       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
       varpl[i][(int)age] =0.;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);       Outputs ps[i][j] the probability to be observed in j being in j according to
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     for(i=1;i<=nlstate;i++)    */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    double s1, lnpijopii;
     /*double t34;*/
     fprintf(ficresvpl,"%.0f ",age );    int i,j, nc, ii, jj;
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      for(i=1; i<= nlstate; i++){
     fprintf(ficresvpl,"\n");        for(j=1; j<i;j++){
     free_vector(gp,1,nlstate);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     free_vector(gm,1,nlstate);            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     free_matrix(gradg,1,npar,1,nlstate);            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     free_matrix(trgradg,1,nlstate,1,npar);  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   } /* End age */          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   free_vector(xp,1,npar);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   free_matrix(doldm,1,nlstate,1,npar);        }
   free_matrix(dnewm,1,nlstate,1,nlstate);        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
 }            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
             lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 /************ Variance of one-step probabilities  ******************/  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          }
 {          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   int i, j;        }
   int k=0, cptcode;      }
   double **dnewm,**doldm;      
   double *xp;      for(i=1; i<= nlstate; i++){
   double *gp, *gm;        s1=0;
   double **gradg, **trgradg;        for(j=1; j<i; j++){
   double age,agelim, cov[NCOVMAX];          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   int theta;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   char fileresprob[FILENAMELENGTH];        }
         for(j=i+1; j<=nlstate+ndeath; j++){
   strcpy(fileresprob,"prob");          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   strcat(fileresprob,fileres);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        }
     printf("Problem with resultfile: %s\n", fileresprob);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   }        ps[i][i]=1./(s1+1.);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        /* Computing other pijs */
          for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
   xp=vector(1,npar);        for(j=i+1; j<=nlstate+ndeath; j++)
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
        } /* end i */
   cov[1]=1;      
   for (age=bage; age<=fage; age ++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     cov[2]=age;        for(jj=1; jj<= nlstate+ndeath; jj++){
     gradg=matrix(1,npar,1,9);          ps[ii][jj]=0;
     trgradg=matrix(1,9,1,npar);          ps[ii][ii]=1;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      }
          
     for(theta=1; theta <=npar; theta++){      
       for(i=1; i<=npar; i++)      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
            /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      /*   } */
          /*   printf("\n "); */
       k=0;      /* } */
       for(i=1; i<= (nlstate+ndeath); i++){      /* printf("\n ");printf("%lf ",cov[2]);*/
         for(j=1; j<=(nlstate+ndeath);j++){      /*
            k=k+1;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           gp[k]=pmmij[i][j];        goto end;*/
         }      return ps;
       }  }
   
       for(i=1; i<=npar; i++)  /**************** Product of 2 matrices ******************/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
      double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   {
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       k=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for(i=1; i<=(nlstate+ndeath); i++){    /* in, b, out are matrice of pointers which should have been initialized 
         for(j=1; j<=(nlstate+ndeath);j++){       before: only the contents of out is modified. The function returns
           k=k+1;       a pointer to pointers identical to out */
           gm[k]=pmmij[i][j];    int i, j, k;
         }    for(i=nrl; i<= nrh; i++)
       }      for(k=ncolol; k<=ncoloh; k++){
              out[i][k]=0.;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        for(j=ncl; j<=nch; j++)
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            out[i][k] +=in[i][j]*b[j][k];
     }      }
     return out;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  }
       for(theta=1; theta <=npar; theta++)  
       trgradg[j][theta]=gradg[theta][j];  
    /************* Higher Matrix Product ***************/
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
      pmij(pmmij,cov,ncovmodel,x,nlstate);    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
      k=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      for(i=1; i<=(nlstate+ndeath); i++){       nhstepm*hstepm matrices. 
        for(j=1; j<=(nlstate+ndeath);j++){       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
          k=k+1;       (typically every 2 years instead of every month which is too big 
          gm[k]=pmmij[i][j];       for the memory).
         }       Model is determined by parameters x and covariates have to be 
      }       included manually here. 
        
      /*printf("\n%d ",(int)age);       */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
            int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    double **newm;
      }*/  
     /* Hstepm could be zero and should return the unit matrix */
   fprintf(ficresprob,"\n%d ",(int)age);    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        po[i][j][0]=(i==j ? 1.0 : 0.0);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      }
   }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      for(d=1; d <=hstepm; d++){
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        newm=savm;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        /* Covariates have to be included here again */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        cov[1]=1.;
 }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
  free_vector(xp,1,npar);        for (k=1; k<=cptcovn;k++) 
 fclose(ficresprob);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
  exit(0);        for (k=1; k<=cptcovage;k++)
 }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
 /******************* Printing html file ***********/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){  
   int jj1, k1, i1, cpt;  
   FILE *fichtm;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   /*char optionfilehtm[FILENAMELENGTH];*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   strcpy(optionfilehtm,optionfile);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   strcat(optionfilehtm,".htm");        savm=oldm;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        oldm=newm;
     printf("Problem with %s \n",optionfilehtm), exit(0);      }
   }      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">          po[i][j][h]=newm[i][j];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
 Total number of observations=%d <br>      /*printf("h=%d ",h);*/
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    } /* end h */
 <hr  size=\"2\" color=\"#EC5E5E\">  /*     printf("\n H=%d \n",h); */
 <li>Outputs files<br><br>\n    return po;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  }
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  #ifdef NLOPT
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    double fret;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    double *xt;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    int j;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    myfunc_data *d2 = (myfunc_data *) pd;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  /* xt = (p1-1); */
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    xt=vector(1,n); 
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
    
 fprintf(fichtm," <li>Graphs</li><p>");    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
  m=cptcoveff;    printf("Function = %.12lf ",fret);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf("\n");
  jj1=0;   free_vector(xt,1,n);
  for(k1=1; k1<=m;k1++){    return fret;
    for(i1=1; i1<=ncodemax[k1];i1++){  }
        jj1++;  #endif
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  /*************** log-likelihood *************/
          for (cpt=1; cpt<=cptcoveff;cpt++)  double func( double *x)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  {
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    int i, ii, j, k, mi, d, kk;
        }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    double **out;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        double sw; /* Sum of weights */
        for(cpt=1; cpt<nlstate;cpt++){    double lli; /* Individual log likelihood */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    int s1, s2;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double bbh, survp;
        }    long ipmx;
     for(cpt=1; cpt<=nlstate;cpt++) {    /*extern weight */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    /* We are differentiating ll according to initial status */
 interval) in state (%d): v%s%d%d.gif <br>    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      /*for(i=1;i<imx;i++) 
      }      printf(" %d\n",s[4][i]);
      for(cpt=1; cpt<=nlstate;cpt++) {    */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    ++countcallfunc;
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    cov[1]=1.;
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    for(k=1; k<=nlstate; k++) ll[k]=0.;
 fprintf(fichtm,"\n</body>");  
    }    if(mle==1){
    }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 fclose(fichtm);        /* Computes the values of the ncovmodel covariates of the model
 }           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
            Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
 /******************* Gnuplot file **************/           to be observed in j being in i according to the model.
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){         */
         for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          cov[2+k]=covar[Tvar[k]][i];
         }
   strcpy(optionfilegnuplot,optionfilefiname);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   strcat(optionfilegnuplot,".plt");           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {           has been calculated etc */
     printf("Problem with file %s",optionfilegnuplot);        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 #ifdef windows              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficgp,"cd \"%s\" \n",pathc);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 #endif            }
 m=pow(2,cptcoveff);          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
  /* 1eme*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (cpt=1; cpt<= nlstate ; cpt ++) {            for (kk=1; kk<=cptcovage;kk++) {
    for (k1=1; k1<= m ; k1 ++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
             }
 #ifdef windows            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #endif            savm=oldm;
 #ifdef unix            oldm=newm;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          } /* end mult */
 #endif        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 for (i=1; i<= nlstate ; i ++) {          /* But now since version 0.9 we anticipate for bias at large stepm.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   else fprintf(ficgp," \%%*lf (\%%*lf)");           * (in months) between two waves is not a multiple of stepm, we rounded to 
 }           * the nearest (and in case of equal distance, to the lowest) interval but now
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for (i=1; i<= nlstate ; i ++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           * probability in order to take into account the bias as a fraction of the way
   else fprintf(ficgp," \%%*lf (\%%*lf)");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 }           * -stepm/2 to stepm/2 .
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);           * For stepm=1 the results are the same as for previous versions of Imach.
      for (i=1; i<= nlstate ; i ++) {           * For stepm > 1 the results are less biased than in previous versions. 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          s1=s[mw[mi][i]][i];
 }            s2=s[mw[mi+1][i]][i];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          bbh=(double)bh[mi][i]/(double)stepm; 
 #ifdef unix          /* bias bh is positive if real duration
 fprintf(ficgp,"\nset ter gif small size 400,300");           * is higher than the multiple of stepm and negative otherwise.
 #endif           */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
    }          if( s2 > nlstate){ 
   }            /* i.e. if s2 is a death state and if the date of death is known 
   /*2 eme*/               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
   for (k1=1; k1<= m ; k1 ++) {               which is also equal to probability to die before dh 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);               minus probability to die before dh-stepm . 
                   In version up to 0.92 likelihood was computed
     for (i=1; i<= nlstate+1 ; i ++) {          as if date of death was unknown. Death was treated as any other
       k=2*i;          health state: the date of the interview describes the actual state
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          and not the date of a change in health state. The former idea was
       for (j=1; j<= nlstate+1 ; j ++) {          to consider that at each interview the state was recorded
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          (healthy, disable or death) and IMaCh was corrected; but when we
   else fprintf(ficgp," \%%*lf (\%%*lf)");          introduced the exact date of death then we should have modified
 }            the contribution of an exact death to the likelihood. This new
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          contribution is smaller and very dependent of the step unit
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          stepm. It is no more the probability to die between last interview
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          and month of death but the probability to survive from last
       for (j=1; j<= nlstate+1 ; j ++) {          interview up to one month before death multiplied by the
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          probability to die within a month. Thanks to Chris
         else fprintf(ficgp," \%%*lf (\%%*lf)");          Jackson for correcting this bug.  Former versions increased
 }            mortality artificially. The bad side is that we add another loop
       fprintf(ficgp,"\" t\"\" w l 0,");          which slows down the processing. The difference can be up to 10%
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          lower mortality.
       for (j=1; j<= nlstate+1 ; j ++) {            */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          /* If, at the beginning of the maximization mostly, the
   else fprintf(ficgp," \%%*lf (\%%*lf)");             cumulative probability or probability to be dead is
 }               constant (ie = 1) over time d, the difference is equal to
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");             0.  out[s1][3] = savm[s1][3]: probability, being at state
       else fprintf(ficgp,"\" t\"\" w l 0,");             s1 at precedent wave, to be dead a month before current
     }             wave is equal to probability, being at state s1 at
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);             precedent wave, to be dead at mont of the current
   }             wave. Then the observed probability (that this person died)
               is null according to current estimated parameter. In fact,
   /*3eme*/             it should be very low but not zero otherwise the log go to
              infinity.
   for (k1=1; k1<= m ; k1 ++) {          */
     for (cpt=1; cpt<= nlstate ; cpt ++) {  /* #ifdef INFINITYORIGINAL */
       k=2+nlstate*(cpt-1);  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  /* #else */
       for (i=1; i< nlstate ; i ++) {  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
         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);  /*          lli=log(mytinydouble); */
       }  /*        else */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
     }  /* #endif */
     }              lli=log(out[s1][s2] - savm[s1][s2]);
    
   /* CV preval stat */          } else if  (s2==-2) {
     for (k1=1; k1<= m ; k1 ++) {            for (j=1,survp=0. ; j<=nlstate; j++) 
     for (cpt=1; cpt<nlstate ; cpt ++) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       k=3;            /*survp += out[s1][j]; */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);            lli= log(survp);
           }
       for (i=1; i< nlstate ; i ++)          
         fprintf(ficgp,"+$%d",k+i+1);          else if  (s2==-4) { 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            for (j=3,survp=0. ; j<=nlstate; j++)  
                    survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       l=3+(nlstate+ndeath)*cpt;            lli= log(survp); 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          } 
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;          else if  (s2==-5) { 
         fprintf(ficgp,"+$%d",l+i+1);            for (j=1,survp=0. ; j<=2; j++)  
       }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              lli= log(survp); 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          } 
     }          
   }            else{
              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   /* proba elementaires */            /*  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(i=1,jk=1; i <=nlstate; i++){          } 
     for(k=1; k <=(nlstate+ndeath); k++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       if (k != i) {          /*if(lli ==000.0)*/
         for(j=1; j <=ncovmodel; j++){          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                  ipmx +=1;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          sw += weight[i];
           jk++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           fprintf(ficgp,"\n");          /* if (lli < log(mytinydouble)){ */
         }          /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
       }          /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
     }          /* } */
     }        } /* end of wave */
       } /* end of individual */
     for(jk=1; jk <=m; jk++) {    }  else if(mle==2){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    i=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
    for(k2=1; k2<=nlstate; k2++) {        for(mi=1; mi<= wav[i]-1; mi++){
      k3=i;          for (ii=1;ii<=nlstate+ndeath;ii++)
      for(k=1; k<=(nlstate+ndeath); k++) {            for (j=1;j<=nlstate+ndeath;j++){
        if (k != k2){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 ij=1;            }
         for(j=3; j <=ncovmodel; j++) {          for(d=0; d<=dh[mi][i]; d++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            newm=savm;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             ij++;            for (kk=1; kk<=cptcovage;kk++) {
           }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           else            }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           fprintf(ficgp,")/(1");            savm=oldm;
                    oldm=newm;
         for(k1=1; k1 <=nlstate; k1++){            } /* end mult */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        
 ij=1;          s1=s[mw[mi][i]][i];
           for(j=3; j <=ncovmodel; j++){          s2=s[mw[mi+1][i]][i];
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          bbh=(double)bh[mi][i]/(double)stepm; 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
             ij++;          ipmx +=1;
           }          sw += weight[i];
           else          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        } /* end of wave */
           }      } /* end of individual */
           fprintf(ficgp,")");    }  else if(mle==3){  /* exponential inter-extrapolation */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        for(mi=1; mi<= wav[i]-1; mi++){
         i=i+ncovmodel;          for (ii=1;ii<=nlstate+ndeath;ii++)
        }            for (j=1;j<=nlstate+ndeath;j++){
      }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            }
    }          for(d=0; d<dh[mi][i]; d++){
                newm=savm;
   fclose(ficgp);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }  /* end gnuplot */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 /*************** Moving average **************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   int i, cpt, cptcod;            oldm=newm;
     for (agedeb=agemin; agedeb<=fage; agedeb++)          } /* end mult */
       for (i=1; i<=nlstate;i++)        
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          s1=s[mw[mi][i]][i];
           mobaverage[(int)agedeb][i][cptcod]=0.;          s2=s[mw[mi+1][i]][i];
              bbh=(double)bh[mi][i]/(double)stepm; 
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){          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 (i=1; i<=nlstate;i++){          ipmx +=1;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          sw += weight[i];
           for (cpt=0;cpt<=4;cpt++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        } /* end of wave */
           }      } /* end of individual */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        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);
 /***********************************************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /**************** Main Program *****************/            }
 /***********************************************/          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 int main(int argc, char *argv[])            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            }
   double agedeb, agefin,hf;          
   double agemin=1.e20, agemax=-1.e20;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double fret;            savm=oldm;
   double **xi,tmp,delta;            oldm=newm;
           } /* end mult */
   double dum; /* Dummy variable */        
   double ***p3mat;          s1=s[mw[mi][i]][i];
   int *indx;          s2=s[mw[mi+1][i]][i];
   char line[MAXLINE], linepar[MAXLINE];          if( s2 > nlstate){ 
   char title[MAXLINE];            lli=log(out[s1][s2] - savm[s1][s2]);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          }else{
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];          ipmx +=1;
           sw += weight[i];
   char filerest[FILENAMELENGTH];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char fileregp[FILENAMELENGTH];  /*      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]); */
   char popfile[FILENAMELENGTH];        } /* end of wave */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      } /* end of individual */
   int firstobs=1, lastobs=10;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   int sdeb, sfin; /* Status at beginning and end */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int c,  h , cpt,l;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int ju,jl, mi;        for(mi=1; mi<= wav[i]-1; mi++){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            for (j=1;j<=nlstate+ndeath;j++){
   int mobilav=0,popforecast=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int hstepm, nhstepm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int *popage;/*boolprev=0 if date and zero if wave*/            }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   double bage, fage, age, agelim, agebase;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ftolpl=FTOL;            for (kk=1; kk<=cptcovage;kk++) {
   double **prlim;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *severity;            }
   double ***param; /* Matrix of parameters */          
   double  *p;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double **matcov; /* Matrix of covariance */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***delti3; /* Scale */            savm=oldm;
   double *delti; /* Scale */            oldm=newm;
   double ***eij, ***vareij;          } /* end mult */
   double **varpl; /* Variances of prevalence limits by age */        
   double *epj, vepp;          s1=s[mw[mi][i]][i];
   double kk1, kk2;          s2=s[mw[mi+1][i]][i];
   double *popeffectif,*popcount;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;          ipmx +=1;
   double yp,yp1,yp2;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";          /*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]);*/
   char *alph[]={"a","a","b","c","d","e"}, str[4];        } /* end of wave */
       } /* end of individual */
     } /* End of if */
   char z[1]="c", occ;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 #include <sys/time.h>    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 #include <time.h>    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    return -l;
    }
   /* long total_usecs;  
   struct timeval start_time, end_time;  /*************** log-likelihood *************/
    double funcone( double *x)
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  {
     /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
   printf("\n%s",version);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   if(argc <=1){    double **out;
     printf("\nEnter the parameter file name: ");    double lli; /* Individual log likelihood */
     scanf("%s",pathtot);    double llt;
   }    int s1, s2;
   else{    double bbh, survp;
     strcpy(pathtot,argv[1]);    /*extern weight */
   }    /* We are differentiating ll according to initial status */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   /*cygwin_split_path(pathtot,path,optionfile);    /*for(i=1;i<imx;i++) 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      printf(" %d\n",s[4][i]);
   /* cutv(path,optionfile,pathtot,'\\');*/    */
     cov[1]=1.;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   chdir(path);  
   replace(pathc,path);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /*-------- arguments in the command line --------*/      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
   strcpy(fileres,"r");          for (j=1;j<=nlstate+ndeath;j++){
   strcat(fileres, optionfilefiname);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(fileres,".txt");    /* Other files have txt extension */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   /*---------arguments file --------*/        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     printf("Problem with optionfile %s\n",optionfile);          for (kk=1; kk<=cptcovage;kk++) {
     goto end;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }          }
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   strcpy(filereso,"o");          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   strcat(filereso,fileres);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if((ficparo=fopen(filereso,"w"))==NULL) {          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   }          savm=oldm;
           oldm=newm;
   /* Reads comments: lines beginning with '#' */        } /* end mult */
   while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        s1=s[mw[mi][i]][i];
     fgets(line, MAXLINE, ficpar);        s2=s[mw[mi+1][i]][i];
     puts(line);        bbh=(double)bh[mi][i]/(double)stepm; 
     fputs(line,ficparo);        /* bias is positive if real duration
   }         * is higher than the multiple of stepm and negative otherwise.
   ungetc(c,ficpar);         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          lli=log(out[s1][s2] - savm[s1][s2]);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        } else if  (s2==-2) {
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);          for (j=1,survp=0. ; j<=nlstate; j++) 
 while((c=getc(ficpar))=='#' && c!= EOF){            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     ungetc(c,ficpar);          lli= log(survp);
     fgets(line, MAXLINE, ficpar);        }else if (mle==1){
     puts(line);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     fputs(line,ficparo);        } else if(mle==2){
   }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   ungetc(c,ficpar);        } else if(mle==3){  /* exponential inter-extrapolation */
            lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
            } else if (mle==4){  /* mle=4 no inter-extrapolation */
   covar=matrix(0,NCOVMAX,1,n);          lli=log(out[s1][s2]); /* Original formula */
   cptcovn=0;        } else{  /* mle=0 back to 1 */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
   ncovmodel=2+cptcovn;        } /* End of if */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        ipmx +=1;
          sw += weight[i];
   /* Read guess parameters */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Reads comments: lines beginning with '#' */        /*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=getc(ficpar))=='#' && c!= EOF){        if(globpr){
     ungetc(c,ficpar);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     fgets(line, MAXLINE, ficpar);   %11.6f %11.6f %11.6f ", \
     puts(line);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     fputs(line,ficparo);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   ungetc(c,ficpar);            llt +=ll[k]*gipmx/gsw;
              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          }
     for(i=1; i <=nlstate; i++)          fprintf(ficresilk," %10.6f\n", -llt);
     for(j=1; j <=nlstate+ndeath-1; j++){        }
       fscanf(ficpar,"%1d%1d",&i1,&j1);      } /* end of wave */
       fprintf(ficparo,"%1d%1d",i1,j1);    } /* end of individual */
       printf("%1d%1d",i,j);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(k=1; k<=ncovmodel;k++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         fscanf(ficpar," %lf",&param[i][j][k]);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         printf(" %lf",param[i][j][k]);    if(globpr==0){ /* First time we count the contributions and weights */
         fprintf(ficparo," %lf",param[i][j][k]);      gipmx=ipmx;
       }      gsw=sw;
       fscanf(ficpar,"\n");    }
       printf("\n");    return -l;
       fprintf(ficparo,"\n");  }
     }  
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   p=param[1][1];  {
      /* This routine should help understanding what is done with 
   /* Reads comments: lines beginning with '#' */       the selection of individuals/waves and
   while((c=getc(ficpar))=='#' && c!= EOF){       to check the exact contribution to the likelihood.
     ungetc(c,ficpar);       Plotting could be done.
     fgets(line, MAXLINE, ficpar);     */
     puts(line);    int k;
     fputs(line,ficparo);  
   }    if(*globpri !=0){ /* Just counts and sums, no printings */
   ungetc(c,ficpar);      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        printf("Problem with resultfile: %s\n", fileresilk);
   for(i=1; i <=nlstate; i++){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     for(j=1; j <=nlstate+ndeath-1; j++){      }
       fscanf(ficpar,"%1d%1d",&i1,&j1);      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");
       printf("%1d%1d",i,j);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       fprintf(ficparo,"%1d%1d",i1,j1);      /*  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; k<=ncovmodel;k++){      for(k=1; k<=nlstate; k++) 
         fscanf(ficpar,"%le",&delti3[i][j][k]);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         printf(" %le",delti3[i][j][k]);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         fprintf(ficparo," %le",delti3[i][j][k]);    }
       }  
       fscanf(ficpar,"\n");    *fretone=(*funcone)(p);
       printf("\n");    if(*globpri !=0){
       fprintf(ficparo,"\n");      fclose(ficresilk);
     }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   }      fflush(fichtm); 
   delti=delti3[1][1];    } 
      return;
   /* Reads comments: lines beginning with '#' */  }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  /*********** Maximum Likelihood Estimation ***************/
     puts(line);  
     fputs(line,ficparo);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   }  {
   ungetc(c,ficpar);    int i,j, iter=0;
      double **xi;
   matcov=matrix(1,npar,1,npar);    double fret;
   for(i=1; i <=npar; i++){    double fretone; /* Only one call to likelihood */
     fscanf(ficpar,"%s",&str);    /*  char filerespow[FILENAMELENGTH];*/
     printf("%s",str);  
     fprintf(ficparo,"%s",str);  #ifdef NLOPT
     for(j=1; j <=i; j++){    int creturn;
       fscanf(ficpar," %le",&matcov[i][j]);    nlopt_opt opt;
       printf(" %.5le",matcov[i][j]);    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
       fprintf(ficparo," %.5le",matcov[i][j]);    double *lb;
     }    double minf; /* the minimum objective value, upon return */
     fscanf(ficpar,"\n");    double * p1; /* Shifted parameters from 0 instead of 1 */
     printf("\n");    myfunc_data dinst, *d = &dinst;
     fprintf(ficparo,"\n");  #endif
   }  
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)    xi=matrix(1,npar,1,npar);
       matcov[i][j]=matcov[j][i];    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++)
   printf("\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     /*-------- data file ----------*/    strcat(filerespow,fileres);
     if((ficres =fopen(fileres,"w"))==NULL) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileres);goto end;      printf("Problem with resultfile: %s\n", filerespow);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     fprintf(ficres,"#%s\n",version);    }
        fprintf(ficrespow,"# Powell\n# iter -2*LL");
     if((fic=fopen(datafile,"r"))==NULL)    {    for (i=1;i<=nlstate;i++)
       printf("Problem with datafile: %s\n", datafile);goto end;      for(j=1;j<=nlstate+ndeath;j++)
     }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
     n= lastobs;  #ifdef POWELL
     severity = vector(1,maxwav);    powell(p,xi,npar,ftol,&iter,&fret,func);
     outcome=imatrix(1,maxwav+1,1,n);  #endif
     num=ivector(1,n);  
     moisnais=vector(1,n);  #ifdef NLOPT
     annais=vector(1,n);  #ifdef NEWUOA
     moisdc=vector(1,n);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
     andc=vector(1,n);  #else
     agedc=vector(1,n);    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
     cod=ivector(1,n);  #endif
     weight=vector(1,n);    lb=vector(0,npar-1);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     mint=matrix(1,maxwav,1,n);    nlopt_set_lower_bounds(opt, lb);
     anint=matrix(1,maxwav,1,n);    nlopt_set_initial_step1(opt, 0.1);
     s=imatrix(1,maxwav+1,1,n);    
     adl=imatrix(1,maxwav+1,1,n);        p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     tab=ivector(1,NCOVMAX);    d->function = func;
     ncodemax=ivector(1,8);    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     nlopt_set_min_objective(opt, myfunc, d);
     i=1;    nlopt_set_xtol_rel(opt, ftol);
     while (fgets(line, MAXLINE, fic) != NULL)    {    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       if ((i >= firstobs) && (i <=lastobs)) {      printf("nlopt failed! %d\n",creturn); 
            }
         for (j=maxwav;j>=1;j--){    else {
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
           strcpy(line,stra);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      iter=1; /* not equal */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    }
         }    nlopt_destroy(opt);
          #endif
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(xi,1,npar,1,npar);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    fclose(ficrespow);
     printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  }
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  /**** Computes Hessian and covariance matrix ***/
         }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         num[i]=atol(stra);  {
            double  **a,**y,*x,pd;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    double **hess;
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    int i, j;
     int *indx;
         i=i+1;  
       }    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);
     /* printf("ii=%d", ij);    void lubksb(double **a, int npar, int *indx, double b[]) ;
        scanf("%d",i);*/    void ludcmp(double **a, int npar, int *indx, double *d) ;
   imx=i-1; /* Number of individuals */    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    printf("\nCalculation of the hessian matrix. Wait...\n");
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    for (i=1;i<=npar;i++){
     }      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
     for (i=1; i<=imx; i++)     
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
   /* Calculation of the number of parameter from char model*/      /*  printf(" %f ",p[i]);
   Tvar=ivector(1,15);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   Tprod=ivector(1,15);    }
   Tvaraff=ivector(1,15);    
   Tvard=imatrix(1,15,1,2);    for (i=1;i<=npar;i++) {
   Tage=ivector(1,15);            for (j=1;j<=npar;j++)  {
            if (j>i) { 
   if (strlen(model) >1){          printf(".%d%d",i,j);fflush(stdout);
     j=0, j1=0, k1=1, k2=1;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     j=nbocc(model,'+');          hess[i][j]=hessij(p,delti,i,j,func,npar);
     j1=nbocc(model,'*');          
     cptcovn=j+1;          hess[j][i]=hess[i][j];    
     cptcovprod=j1;          /*printf(" %lf ",hess[i][j]);*/
            }
          }
     strcpy(modelsav,model);    }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    printf("\n");
       printf("Error. Non available option model=%s ",model);    fprintf(ficlog,"\n");
       goto end;  
     }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
        fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(i=(j+1); i>=1;i--){    
       cutv(stra,strb,modelsav,'+');    a=matrix(1,npar,1,npar);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    y=matrix(1,npar,1,npar);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    x=vector(1,npar);
       /*scanf("%d",i);*/    indx=ivector(1,npar);
       if (strchr(strb,'*')) {    for (i=1;i<=npar;i++)
         cutv(strd,strc,strb,'*');      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         if (strcmp(strc,"age")==0) {    ludcmp(a,npar,indx,&pd);
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    for (j=1;j<=npar;j++) {
           Tvar[i]=atoi(stre);      for (i=1;i<=npar;i++) x[i]=0;
           cptcovage++;      x[j]=1;
             Tage[cptcovage]=i;      lubksb(a,npar,indx,x);
             /*printf("stre=%s ", stre);*/      for (i=1;i<=npar;i++){ 
         }        matcov[i][j]=x[i];
         else if (strcmp(strd,"age")==0) {      }
           cptcovprod--;    }
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);    printf("\n#Hessian matrix#\n");
           cptcovage++;    fprintf(ficlog,"\n#Hessian matrix#\n");
           Tage[cptcovage]=i;    for (i=1;i<=npar;i++) { 
         }      for (j=1;j<=npar;j++) { 
         else {        printf("%.3e ",hess[i][j]);
           cutv(strb,stre,strc,'V');        fprintf(ficlog,"%.3e ",hess[i][j]);
           Tvar[i]=ncov+k1;      }
           cutv(strb,strc,strd,'V');      printf("\n");
           Tprod[k1]=i;      fprintf(ficlog,"\n");
           Tvard[k1][1]=atoi(strc);    }
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];    /* Recompute Inverse */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    for (i=1;i<=npar;i++)
           for (k=1; k<=lastobs;k++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    ludcmp(a,npar,indx,&pd);
           k1++;  
           k2=k2+2;    /*  printf("\n#Hessian matrix recomputed#\n");
         }  
       }    for (j=1;j<=npar;j++) {
       else {      for (i=1;i<=npar;i++) x[i]=0;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      x[j]=1;
        /*  scanf("%d",i);*/      lubksb(a,npar,indx,x);
       cutv(strd,strc,strb,'V');      for (i=1;i<=npar;i++){ 
       Tvar[i]=atoi(strc);        y[i][j]=x[i];
       }        printf("%.3e ",y[i][j]);
       strcpy(modelsav,stra);          fprintf(ficlog,"%.3e ",y[i][j]);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      }
         scanf("%d",i);*/      printf("\n");
     }      fprintf(ficlog,"\n");
 }    }
      */
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  
   printf("cptcovprod=%d ", cptcovprod);    free_matrix(a,1,npar,1,npar);
   scanf("%d ",i);*/    free_matrix(y,1,npar,1,npar);
     fclose(fic);    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     /*  if(mle==1){*/    free_matrix(hess,1,npar,1,npar);
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }  }
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
    for (i=1; i<=imx; i++)  {
      for(m=2; (m<= maxwav); m++)    int i;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    int l=1, lmax=20;
          anint[m][i]=9999;    double k1,k2;
          s[m][i]=-1;    double p2[MAXPARM+1]; /* identical to x */
        }    double res;
        double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     for (i=1; i<=imx; i++)  {    double fx;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    int k=0,kmax=10;
       for(m=1; (m<= maxwav); m++){    double l1;
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {    fx=func(x);
             if(agedc[i]>0)    for (i=1;i<=npar;i++) p2[i]=x[i];
               if(moisdc[i]!=99 && andc[i]!=9999)    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
               agev[m][i]=agedc[i];      l1=pow(10,l);
             else {      delts=delt;
               if (andc[i]!=9999){      for(k=1 ; k <kmax; k=k+1){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        delt = delta*(l1*k);
               agev[m][i]=-1;        p2[theta]=x[theta] +delt;
               }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
             }        p2[theta]=x[theta]-delt;
           }        k2=func(p2)-fx;
           else if(s[m][i] !=9){ /* Should no more exist */        /*res= (k1-2.0*fx+k2)/delt/delt; */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
             if(mint[m][i]==99 || anint[m][i]==9999)        
               agev[m][i]=1;  #ifdef DEBUGHESS
             else if(agev[m][i] <agemin){        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);
               agemin=agev[m][i];        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);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  #endif
             }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
             else if(agev[m][i] >agemax){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
               agemax=agev[m][i];          k=kmax;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        }
             }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             /*agev[m][i]=anint[m][i]-annais[i];*/          k=kmax; l=lmax*10;
             /*   agev[m][i] = age[i]+2*m;*/        }
           }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           else { /* =9 */          delts=delt;
             agev[m][i]=1;        }
             s[m][i]=-1;      }
           }    }
         }    delti[theta]=delts;
         else /*= 0 Unknown */    return res; 
           agev[m][i]=1;    
       }  }
      
     }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     for (i=1; i<=imx; i++)  {  {
       for(m=1; (m<= maxwav); m++){    int i;
         if (s[m][i] > (nlstate+ndeath)) {    int l=1, lmax=20;
           printf("Error: Wrong value in nlstate or ndeath\n");      double k1,k2,k3,k4,res,fx;
           goto end;    double p2[MAXPARM+1];
         }    int k;
       }  
     }    fx=func(x);
     for (k=1; k<=2; k++) {
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
     free_vector(severity,1,maxwav);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     free_imatrix(outcome,1,maxwav+1,1,n);      k1=func(p2)-fx;
     free_vector(moisnais,1,n);    
     free_vector(annais,1,n);      p2[thetai]=x[thetai]+delti[thetai]/k;
     /* free_matrix(mint,1,maxwav,1,n);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        free_matrix(anint,1,maxwav,1,n);*/      k2=func(p2)-fx;
     free_vector(moisdc,1,n);    
     free_vector(andc,1,n);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          k3=func(p2)-fx;
     wav=ivector(1,imx);    
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      p2[thetai]=x[thetai]-delti[thetai]/k;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          k4=func(p2)-fx;
     /* Concatenates waves */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       Tcode=ivector(1,100);  #endif
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    }
       ncodemax[1]=1;    return res;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  }
        
    codtab=imatrix(1,100,1,10);  /************** Inverse of matrix **************/
    h=0;  void ludcmp(double **a, int n, int *indx, double *d) 
    m=pow(2,cptcoveff);  { 
      int i,imax,j,k; 
    for(k=1;k<=cptcoveff; k++){    double big,dum,sum,temp; 
      for(i=1; i <=(m/pow(2,k));i++){    double *vv; 
        for(j=1; j <= ncodemax[k]; j++){   
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    vv=vector(1,n); 
            h++;    *d=1.0; 
            if (h>m) h=1;codtab[h][k]=j;    for (i=1;i<=n;i++) { 
          }      big=0.0; 
        }      for (j=1;j<=n;j++) 
      }        if ((temp=fabs(a[i][j])) > big) big=temp; 
    }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
     } 
    /*for(i=1; i <=m ;i++){    for (j=1;j<=n;j++) { 
      for(k=1; k <=cptcovn; k++){      for (i=1;i<j;i++) { 
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        sum=a[i][j]; 
      }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      printf("\n");        a[i][j]=sum; 
    }      } 
    scanf("%d",i);*/      big=0.0; 
          for (i=j;i<=n;i++) { 
    /* Calculates basic frequencies. Computes observed prevalence at single age        sum=a[i][j]; 
        and prints on file fileres'p'. */        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
            a[i][j]=sum; 
            if ( (dum=vv[i]*fabs(sum)) >= big) { 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          big=dum; 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          imax=i; 
     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 */      if (j != imax) { 
              for (k=1;k<=n;k++) { 
     /* For Powell, parameters are in a vector p[] starting at p[1]          dum=a[imax][k]; 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          a[imax][k]=a[j][k]; 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          a[j][k]=dum; 
         } 
     if(mle==1){        *d = -(*d); 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        vv[imax]=vv[j]; 
     }      } 
          indx[j]=imax; 
     /*--------- results files --------------*/      if (a[j][j] == 0.0) a[j][j]=TINY; 
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);      if (j != n) { 
          dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
    jk=1;      } 
    fprintf(ficres,"# Parameters\n");    } 
    printf("# Parameters\n");    free_vector(vv,1,n);  /* Doesn't work */
    for(i=1,jk=1; i <=nlstate; i++){  ;
      for(k=1; k <=(nlstate+ndeath); k++){  } 
        if (k != i)  
          {  void lubksb(double **a, int n, int *indx, double b[]) 
            printf("%d%d ",i,k);  { 
            fprintf(ficres,"%1d%1d ",i,k);    int i,ii=0,ip,j; 
            for(j=1; j <=ncovmodel; j++){    double sum; 
              printf("%f ",p[jk]);   
              fprintf(ficres,"%f ",p[jk]);    for (i=1;i<=n;i++) { 
              jk++;      ip=indx[i]; 
            }      sum=b[ip]; 
            printf("\n");      b[ip]=b[i]; 
            fprintf(ficres,"\n");      if (ii) 
          }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
      }      else if (sum) ii=i; 
    }      b[i]=sum; 
  if(mle==1){    } 
     /* Computing hessian and covariance matrix */    for (i=n;i>=1;i--) { 
     ftolhess=ftol; /* Usually correct */      sum=b[i]; 
     hesscov(matcov, p, npar, delti, ftolhess, func);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
  }      b[i]=sum/a[i][i]; 
     fprintf(ficres,"# Scales\n");    } 
     printf("# Scales\n");  } 
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){  void pstamp(FILE *fichier)
         if (j!=i) {  {
           fprintf(ficres,"%1d%1d",i,j);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
           printf("%1d%1d",i,j);  }
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);  /************ Frequencies ********************/
             fprintf(ficres," %.5e",delti[jk]);  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[])
             jk++;  {  /* Some frequencies */
           }    
           printf("\n");    int i, m, jk, j1, bool, z1,j;
           fprintf(ficres,"\n");    int first;
         }    double ***freq; /* Frequencies */
       }    double *pp, **prop;
      }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        char fileresp[FILENAMELENGTH];
     k=1;    
     fprintf(ficres,"# Covariance\n");    pp=vector(1,nlstate);
     printf("# Covariance\n");    prop=matrix(1,nlstate,iagemin,iagemax+3);
     for(i=1;i<=npar;i++){    strcpy(fileresp,"p");
       /*  if (k>nlstate) k=1;    strcat(fileresp,fileres);
       i1=(i-1)/(ncovmodel*nlstate)+1;    if((ficresp=fopen(fileresp,"w"))==NULL) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      printf("Problem with prevalence resultfile: %s\n", fileresp);
       printf("%s%d%d",alph[k],i1,tab[i]);*/      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficres,"%3d",i);      exit(0);
       printf("%3d",i);    }
       for(j=1; j<=i;j++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
         fprintf(ficres," %.5e",matcov[i][j]);    j1=0;
         printf(" %.5e",matcov[i][j]);    
       }    j=cptcoveff;
       fprintf(ficres,"\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       printf("\n");  
       k++;    first=1;
     }  
        /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
     while((c=getc(ficpar))=='#' && c!= EOF){    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
       ungetc(c,ficpar);    /*    j1++; */
       fgets(line, MAXLINE, ficpar);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       puts(line);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       fputs(line,ficparo);          scanf("%d", i);*/
     }        for (i=-5; i<=nlstate+ndeath; i++)  
     ungetc(c,ficpar);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
              for(m=iagemin; m <= iagemax+3; m++)
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              freq[i][jk][m]=0;
            
     if (fage <= 2) {        for (i=1; i<=nlstate; i++)  
       bage = agemin;          for(m=iagemin; m <= iagemax+3; m++)
       fage = agemax;            prop[i][m]=0;
     }        
            dateintsum=0;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        k2cpt=0;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        for (i=1; i<=imx; i++) {
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          bool=1;
            if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
     while((c=getc(ficpar))=='#' && c!= EOF){            for (z1=1; z1<=cptcoveff; z1++)       
     ungetc(c,ficpar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
     fgets(line, MAXLINE, ficpar);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
     puts(line);                bool=0;
     fputs(line,ficparo);                /* 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", 
   }                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
   ungetc(c,ficpar);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
                  /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);              } 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   
                if (bool==1){
   while((c=getc(ficpar))=='#' && c!= EOF){            for(m=firstpass; m<=lastpass; m++){
     ungetc(c,ficpar);              k2=anint[m][i]+(mint[m][i]/12.);
     fgets(line, MAXLINE, ficpar);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     puts(line);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fputs(line,ficparo);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   ungetc(c,ficpar);                if (m<lastpass) {
                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   fscanf(ficpar,"pop_based=%d\n",&popbased);                  dateintsum=dateintsum+k2;
    fprintf(ficparo,"pop_based=%d\n",popbased);                    k2cpt++;
    fprintf(ficres,"pop_based=%d\n",popbased);                  }
                 /*}*/
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        } /* end i */
     puts(line);         
     fputs(line,ficparo);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   }        pstamp(ficresp);
   ungetc(c,ficpar);        if  (cptcovn>0) {
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mob_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          fprintf(ficresp, "\n#********** Variable "); 
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          fprintf(ficresp, "**********\n#");
           fprintf(ficlog, "\n#********** Variable "); 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficlog, "**********\n#");
 /*------------ gnuplot -------------*/        }
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);        for(i=1; i<=nlstate;i++) 
            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 /*------------ free_vector  -------------*/        fprintf(ficresp, "\n");
  chdir(path);        
          for(i=iagemin; i <= iagemax+3; i++){
  free_ivector(wav,1,imx);          if(i==iagemax+3){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            fprintf(ficlog,"Total");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            }else{
  free_ivector(num,1,n);            if(first==1){
  free_vector(agedc,1,n);              first=0;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/              printf("See log file for details...\n");
  fclose(ficparo);            }
  fclose(ficres);            fprintf(ficlog,"Age %d", i);
            }
   /* Reads comments: lines beginning with '#' */          for(jk=1; jk <=nlstate ; jk++){
   while((c=getc(ficpar))=='#' && c!= EOF){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     ungetc(c,ficpar);              pp[jk] += freq[jk][m][i]; 
     fgets(line, MAXLINE, ficpar);          }
     puts(line);          for(jk=1; jk <=nlstate ; jk++){
     fputs(line,ficparo);            for(m=-1, pos=0; m <=0 ; m++)
   }              pos += freq[jk][m][i];
   ungetc(c,ficpar);            if(pp[jk]>=1.e-10){
                if(first==1){
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 /*--------- index.htm --------*/            }else{
               if(first==1)
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
   /*--------------- Prevalence limit --------------*/          }
    
   strcpy(filerespl,"pl");          for(jk=1; jk <=nlstate ; jk++){
   strcat(filerespl,fileres);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {              pp[jk] += freq[jk][m][i];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          }       
   }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            pos += pp[jk];
   fprintf(ficrespl,"#Prevalence limit\n");            posprop += prop[jk][i];
   fprintf(ficrespl,"#Age ");          }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficrespl,"\n");            if(pos>=1.e-5){
                if(first==1)
   prlim=matrix(1,nlstate,1,nlstate);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   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 prev[%d]=NaNQ%%",jk,pp[jk],jk);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   k=0;            }
   agebase=agemin;            if( i <= iagemax){
   agelim=agemax;              if(pos>=1.e-5){
   ftolpl=1.e-10;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   i1=cptcoveff;                /*probs[i][jk][j1]= pp[jk]/pos;*/
   if (cptcovn < 1){i1=1;}                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
   for(cptcov=1;cptcov<=i1;cptcov++){              else
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         k=k+1;            }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          }
         fprintf(ficrespl,"\n#******");          
         for(j=1;j<=cptcoveff;j++)          for(jk=-1; jk <=nlstate+ndeath; jk++)
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(m=-1; m <=nlstate+ndeath; m++)
         fprintf(ficrespl,"******\n");              if(freq[jk][m][i] !=0 ) {
                      if(first==1)
         for (age=agebase; age<=agelim; age++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           fprintf(ficrespl,"%.0f",age );              }
           for(i=1; i<=nlstate;i++)          if(i <= iagemax)
           fprintf(ficrespl," %.5f", prlim[i][i]);            fprintf(ficresp,"\n");
           fprintf(ficrespl,"\n");          if(first==1)
         }            printf("Others in log...\n");
       }          fprintf(ficlog,"\n");
     }        }
   fclose(ficrespl);        /*}*/
     }
   /*------------- h Pij x at various ages ------------*/    dateintmean=dateintsum/k2cpt; 
     
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    fclose(ficresp);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    free_vector(pp,1,nlstate);
   }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   printf("Computing pij: result on file '%s' \n", filerespij);    /* End of Freq */
    }
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/  /************ Prevalence ********************/
   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)
   agelim=AGESUP;  {  
   hstepm=stepsize*YEARM; /* Every year of age */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       in each health status at the date of interview (if between dateprev1 and dateprev2).
         We still use firstpass and lastpass as another selection.
   k=0;    */
   for(cptcov=1;cptcov<=i1;cptcov++){   
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int i, m, jk, j1, bool, z1,j;
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");    double **prop;
         for(j=1;j<=cptcoveff;j++)    double posprop; 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double  y2; /* in fractional years */
         fprintf(ficrespij,"******\n");    int iagemin, iagemax;
            int first; /** to stop verbosity which is redirected to log file */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    iagemin= (int) agemin;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    iagemax= (int) agemax;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*pp=vector(1,nlstate);*/
           oldm=oldms;savm=savms;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           fprintf(ficrespij,"# Age");    j1=0;
           for(i=1; i<=nlstate;i++)    
             for(j=1; j<=nlstate+ndeath;j++)    /*j=cptcoveff;*/
               fprintf(ficrespij," %1d-%1d",i,j);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           fprintf(ficrespij,"\n");    
           for (h=0; h<=nhstepm; h++){    first=1;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
             for(i=1; i<=nlstate;i++)      /*for(i1=1; i1<=ncodemax[k1];i1++){
               for(j=1; j<=nlstate+ndeath;j++)        j1++;*/
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        
             fprintf(ficrespij,"\n");        for (i=1; i<=nlstate; i++)  
           }          for(m=iagemin; m <= iagemax+3; m++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            prop[i][m]=0.0;
           fprintf(ficrespij,"\n");       
         }        for (i=1; i<=imx; i++) { /* Each individual */
     }          bool=1;
   }          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
   fclose(ficrespij);          } 
           if (bool==1) { 
   if(stepm == 1) {            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   /*---------- Forecasting ------------------*/              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /*printf("calage= %f", calagedate);*/                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); 
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
   strcpy(fileresf,"f");                  prop[s[m][i]][iagemax+3] += weight[i]; 
   strcat(fileresf,fileres);                } 
   if((ficresf=fopen(fileresf,"w"))==NULL) {              }
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;            } /* end selection of waves */
   }          }
   printf("Computing forecasting: result on file '%s' \n", fileresf);        }
         for(i=iagemin; i <= iagemax+3; i++){  
   free_matrix(mint,1,maxwav,1,n);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   free_matrix(anint,1,maxwav,1,n);            posprop += prop[jk][i]; 
   free_matrix(agev,1,maxwav,1,imx);          } 
           
   /* Mobile average */          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
   if (mobilav==1) {              } else{
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                if(first==1){
     movingaverage(agedeb, fage, agemin, mobaverage);                  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]);
                 }
   stepsize=(int) (stepm+YEARM-1)/YEARM;              }
   if (stepm<=12) stepsize=1;            } 
           }/* end jk */ 
   agelim=AGESUP;        }/* end i */ 
   /*hstepm=stepsize*YEARM; *//* Every year of age */      /*} *//* end i1 */
   hstepm=1;    } /* end j1 */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    
   yp1=modf(dateintmean,&yp);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   anprojmean=yp;    /*free_vector(pp,1,nlstate);*/
   yp2=modf((yp1*12),&yp);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   mprojmean=yp;  }  /* End of prevalence */
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;  /************* Waves Concatenation ***************/
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;  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(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
   if (popforecast==1) {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     if((ficpop=fopen(popfile,"r"))==NULL)    {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       printf("Problem with population file : %s\n",popfile);goto end;       and mw[mi+1][i]. dh depends on stepm.
     }       */
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);    int i, mi, m;
     popcount=vector(0,AGESUP);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
     i=1;      int first;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)    int j, k=0,jk, ju, jl;
       {    double sum=0.;
         i=i+1;    first=0;
       }    jmin=100000;
     imx=i;    jmax=-1;
        jmean=0.;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    for(i=1; i<=imx; i++){
   }      mi=0;
       m=firstpass;
   for(cptcov=1;cptcov<=i1;cptcov++){      while(s[m][i] <= nlstate){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       k=k+1;          mw[++mi][i]=m;
       fprintf(ficresf,"\n#******");        if(m >=lastpass)
       for(j=1;j<=cptcoveff;j++) {          break;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        else
       }          m++;
       fprintf(ficresf,"******\n");      }/* end while */
       fprintf(ficresf,"# StartingAge FinalAge");      if (s[m][i] > nlstate){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        mi++;     /* Death is another wave */
       if (popforecast==1)  fprintf(ficresf," [Population]");        /* if(mi==0)  never been interviewed correctly before death */
                 /* Only death is a correct wave */
      for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        mw[mi][i]=m;
         fprintf(ficresf,"\n");      }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
       wav[i]=mi;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      if(mi==0){
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        nbwarn++;
         nhstepm = nhstepm/hstepm;        if(first==0){
                  printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          first=1;
         oldm=oldms;savm=savms;        }
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          if(first==1){
                  fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         for (h=0; h<=nhstepm; h++){        }
           if (h==(int) (calagedate+YEARM*cpt)) {      } /* end mi==0 */
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    } /* End individuals */
           }  
           for(j=1; j<=nlstate+ndeath;j++) {    for(i=1; i<=imx; i++){
             kk1=0.;kk2=0;      for(mi=1; mi<wav[i];mi++){
             for(i=1; i<=nlstate;i++) {                if (stepm <=0)
               if (mobilav==1)          dh[mi][i]=1;
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        else{
               else {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            if (agedc[i] < 2*AGESUP) {
                              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               }              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];                nberr++;
             }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                          j=1; /* Temporary Dangerous patch */
             if (h==(int)(calagedate+12*cpt)){                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               fprintf(ficresf," %.3f", kk1);                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(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);              }
             }              k=k+1;
           }              if (j >= jmax){
         }                jmax=j;
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                ijmax=i;
         }              }
      }              if (j <= jmin){
     }                jmin=j;
   }                ijmin=i;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              }
               sum=sum+j;
   if (popforecast==1) {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     free_ivector(popage,0,AGESUP);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     free_vector(popeffectif,0,AGESUP);            }
     free_vector(popcount,0,AGESUP);          }
   }          else{
   free_imatrix(s,1,maxwav+1,1,n);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   free_vector(weight,1,n);  /*        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]); */
   fclose(ficresf);  
   }/* End forecasting */            k=k+1;
   else{            if (j >= jmax) {
     erreur=108;              jmax=j;
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);              ijmax=i;
             }
   }            else if (j <= jmin){
               jmin=j;
                ijmin=i;
   /*---------- Health expectancies and variances ------------*/            }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   strcpy(filerest,"t");            /*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]);*/
   strcat(filerest,fileres);            if(j<0){
   if((ficrest=fopen(filerest,"w"))==NULL) {              nberr++;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            }
             sum=sum+j;
           }
   strcpy(filerese,"e");          jk= j/stepm;
   strcat(filerese,fileres);          jl= j -jk*stepm;
   if((ficreseij=fopen(filerese,"w"))==NULL) {          ju= j -(jk+1)*stepm;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   }            if(jl==0){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);              dh[mi][i]=jk;
               bh[mi][i]=0;
  strcpy(fileresv,"v");            }else{ /* We want a negative bias in order to only have interpolation ie
   strcat(fileresv,fileres);                    * to avoid the price of an extra matrix product in likelihood */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {              dh[mi][i]=jk+1;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);              bh[mi][i]=ju;
   }            }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          }else{
             if(jl <= -ju){
   k=0;              dh[mi][i]=jk;
   for(cptcov=1;cptcov<=i1;cptcov++){              bh[mi][i]=jl;       /* bias is positive if real duration
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                                   * is higher than the multiple of stepm and negative otherwise.
       k=k+1;                                   */
       fprintf(ficrest,"\n#****** ");            }
       for(j=1;j<=cptcoveff;j++)            else{
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              dh[mi][i]=jk+1;
       fprintf(ficrest,"******\n");              bh[mi][i]=ju;
             }
       fprintf(ficreseij,"\n#****** ");            if(dh[mi][i]==0){
       for(j=1;j<=cptcoveff;j++)              dh[mi][i]=1; /* At least one step */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);              bh[mi][i]=ju; /* At least one step */
       fprintf(ficreseij,"******\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);*/
             }
       fprintf(ficresvij,"\n#****** ");          } /* end if mle */
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      } /* end wave */
       fprintf(ficresvij,"******\n");    }
     jmean=sum/k;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    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);
       oldm=oldms;savm=savms;    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);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);     }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  /*********** Tricode ****************************/
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
        {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
       fprintf(ficrest,"\n");     * Boring subroutine which should only output nbcode[Tvar[j]][k]
             * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       hf=1;     * nbcode[Tvar[j]][1]= 
       if (stepm >= YEARM) hf=stepm/YEARM;    */
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    int modmaxcovj=0; /* Modality max of covariates j */
         if (popbased==1) {    int cptcode=0; /* Modality max of covariates j */
           for(i=1; i<=nlstate;i++)    int modmincovj=0; /* Modality min of covariates j */
             prlim[i][i]=probs[(int)age][i][k];  
         }  
            cptcoveff=0; 
         fprintf(ficrest," %.0f",age);   
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    for (k=-1; k < maxncov; k++) Ndum[k]=0;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  
           }    /* Loop on covariates without age and products */
           epj[nlstate+1] +=epj[j];    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
         }      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
         for(i=1, vepp=0.;i <=nlstate;i++)                                 modality of this covariate Vj*/ 
           for(j=1;j <=nlstate;j++)        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
             vepp += vareij[i][j][(int)age];                                      * If product of Vn*Vm, still boolean *:
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
         for(j=1;j <=nlstate;j++){                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
         }                                        modality of the nth covariate of individual i. */
         fprintf(ficrest,"\n");        if (ij > modmaxcovj)
       }          modmaxcovj=ij; 
     }        else if (ij < modmincovj) 
   }          modmincovj=ij; 
                if ((ij < -1) && (ij > NCOVMAX)){
                  printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
           exit(1);
         }else
  fclose(ficreseij);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
  fclose(ficresvij);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   fclose(ficrest);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   fclose(ficpar);        /* getting the maximum value of the modality of the covariate
   free_vector(epj,1,nlstate+1);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   /*  scanf("%d ",i); */           female is 1, then modmaxcovj=1.*/
       }
   /*------- Variance limit prevalence------*/        printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       cptcode=modmaxcovj;
 strcpy(fileresvpl,"vpl");      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   strcat(fileresvpl,fileres);     /*for (i=0; i<=cptcode; i++) {*/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
     exit(0);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
   }          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        }
         /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
  k=0;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
  for(cptcov=1;cptcov<=i1;cptcov++){      } /* Ndum[-1] number of undefined modalities */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
      fprintf(ficresvpl,"\n#****** ");      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
      for(j=1;j<=cptcoveff;j++)      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         modmincovj=3; modmaxcovj = 7;
      fprintf(ficresvpl,"******\n");         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
               which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
      varpl=matrix(1,nlstate,(int) bage, (int) fage);         variables V1_1 and V1_2.
      oldm=oldms;savm=savms;         nbcode[Tvar[j]][ij]=k;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         nbcode[Tvar[j]][1]=0;
    }         nbcode[Tvar[j]][2]=1;
  }         nbcode[Tvar[j]][3]=2;
       */
   fclose(ficresvpl);      ij=1; /* ij is similar to i but can jumps over null modalities */
       for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
   /*---------- End : free ----------------*/        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          /*recode from 0 */
            if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                                       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++;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          }
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          if (ij > ncodemax[j]) break; 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        }  /* end of loop on */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      } /* end of loop on modality */ 
      } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   free_matrix(matcov,1,npar,1,npar);    
   free_vector(delti,1,npar);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
      
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   if(erreur >0)     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     printf("End of Imach with error %d\n",erreur);     Ndum[ij]++; 
   else   printf("End of Imach\n");   } 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
     ij=1;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   /*printf("Total time was %d uSec.\n", total_usecs);*/     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   /*------ End -----------*/     if((Ndum[i]!=0) && (i<=ncovcol)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
  end:       ij++;
 #ifdef windows     }else
   /* chdir(pathcd);*/         Tvaraff[ij]=0;
 #endif   }
  /*system("wgnuplot graph.plt");*/   ij--;
  /*system("../gp37mgw/wgnuplot graph.plt");*/   cptcoveff=ij; /*Number of total covariates*/
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  }
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);  /*********** Health Expectancies ****************/
  system(plotcmd);  
   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
 #ifdef windows  
   while (z[0] != 'q') {  {
     chdir(path);    /* Health expectancies, no variances */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    int i, j, nhstepm, hstepm, h, nstepm;
     scanf("%s",z);    int nhstepma, nstepma; /* Decreasing with age */
     if (z[0] == 'c') system("./imach");    double age, agelim, hf;
     else if (z[0] == 'e') {    double ***p3mat;
       chdir(path);    double eip;
       system(optionfilehtm);  
     }    pstamp(ficreseij);
     else if (z[0] == 'q') exit(0);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   }    fprintf(ficreseij,"# Age");
 #endif    for(i=1; i<=nlstate;i++){
 }      for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       }
       fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficreseij,"\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 */ 
   
     agelim=AGESUP;
     /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* 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;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
           /* command line Intel compiler 64bit windows:
           /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" */
           /*
           /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" */
   #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 --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
   #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*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
   #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.1.25  
changed lines
  Added in v.1.184


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