Diff for /imach/src/imach.c between versions 1.46 and 1.187

version 1.46, 2002/05/30 17:44:35 version 1.187, 2015/04/29 09:11:15
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.187  2015/04/29 09:11:15  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.186  2015/04/23 12:01:52  brouard
   first survey ("cross") where individuals from different ages are    Summary: V1*age is working now, version 0.98q1
   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    Some codes had been disabled in order to simplify and Vn*age was
   second wave of interviews ("longitudinal") which measure each change    working in the optimization phase, ie, giving correct MLE parameters,
   (if any) in individual health status.  Health expectancies are    but, as usual, outputs were not correct and program core dumped.
   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    Revision 1.185  2015/03/11 13:26:42  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Summary: Inclusion of compile and links command line for Intel Compiler
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.184  2015/03/11 11:52:39  brouard
   conditional to be observed in state i at the first wave. Therefore    Summary: Back from Windows 8. Intel Compiler
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.183  2015/03/10 20:34:32  brouard
   complex model than "constant and age", you should modify the program    Summary: 0.98q0, trying with directest, mnbrak fixed
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    We use directest instead of original Powell test; probably no
   convergence.    incidence on the results, but better justifications;
     We fixed Numerical Recipes mnbrak routine which was wrong and gave
   The advantage of this computer programme, compared to a simple    wrong results.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.182  2015/02/12 08:19:57  brouard
   intermediate interview, the information is lost, but taken into    Summary: Trying to keep directest which seems simpler and more general
   account using an interpolation or extrapolation.      Author: Nicolas Brouard
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.181  2015/02/11 23:22:24  brouard
   conditional to the observed state i at age x. The delay 'h' can be    Summary: Comments on Powell added
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Author:
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.180  2015/02/11 17:33:45  brouard
   and the contribution of each individual to the likelihood is simply    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   hPijx.  
     Revision 1.179  2015/01/04 09:57:06  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Summary: back to OS/X
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.178  2015/01/04 09:35:48  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    *** empty log message ***
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.177  2015/01/03 18:40:56  brouard
   from the European Union.    Summary: Still testing ilc32 on OSX
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.176  2015/01/03 16:45:04  brouard
   can be accessed at http://euroreves.ined.fr/imach .    *** empty log message ***
   **********************************************************************/  
      Revision 1.175  2015/01/03 16:33:42  brouard
 #include <math.h>    *** empty log message ***
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.174  2015/01/03 16:15:49  brouard
 #include <unistd.h>    Summary: Still in cross-compilation
   
 #define MAXLINE 256    Revision 1.173  2015/01/03 12:06:26  brouard
 #define GNUPLOTPROGRAM "gnuplot"    Summary: trying to detect cross-compilation
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.172  2014/12/27 12:07:47  brouard
 /*#define DEBUG*/    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.171  2014/12/23 13:26:59  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Summary: Back from Visual C
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Still problem with utsname.h on Windows
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.170  2014/12/23 11:17:12  brouard
 #define NINTERVMAX 8    Summary: Cleaning some \%% back to %%
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.169  2014/12/22 23:08:31  brouard
 #define YEARM 12. /* Number of months per year */    Summary: 0.98p
 #define AGESUP 130  
 #define AGEBASE 40    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
     Revision 1.168  2014/12/22 15:17:42  brouard
 int erreur; /* Error number */    Summary: update
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.167  2014/12/22 13:50:56  brouard
 int npar=NPARMAX;    Summary: Testing uname and compiler version and if compiled 32 or 64
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Testing on Linux 64
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.166  2014/12/22 11:40:47  brouard
     *** empty log message ***
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.165  2014/12/16 11:20:36  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    Summary: After compiling on Visual C
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    * imach.c (Module): Merging 1.61 to 1.162
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.164  2014/12/16 10:52:11  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    * imach.c (Module): Merging 1.61 to 1.162
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficreseij;    Revision 1.163  2014/12/16 10:30:11  brouard
   char filerese[FILENAMELENGTH];    * imach.c (Module): Merging 1.61 to 1.162
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.162  2014/09/25 11:43:39  brouard
  FILE  *ficresvpl;    Summary: temporary backup 0.99!
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.1  2014/09/16 11:06:58  brouard
 #define NR_END 1    Summary: With some code (wrong) for nlopt
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Author:
   
 #define NRANSI    Revision 1.161  2014/09/15 20:41:41  brouard
 #define ITMAX 200    Summary: Problem with macro SQR on Intel compiler
   
 #define TOL 2.0e-4    Revision 1.160  2014/09/02 09:24:05  brouard
     *** empty log message ***
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.159  2014/09/01 10:34:10  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Summary: WIN32
     Author: Brouard
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.158  2014/08/27 17:11:51  brouard
 #define TINY 1.0e-20    *** empty log message ***
   
 static double maxarg1,maxarg2;    Revision 1.157  2014/08/27 16:26:55  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Summary: Preparing windows Visual studio version
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Author: Brouard
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    In order to compile on Visual studio, time.h is now correct and time_t
 #define rint(a) floor(a+0.5)    and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
 static double sqrarg;    Trying to suppress #ifdef LINUX
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Add xdg-open for __linux in order to open default browser.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.156  2014/08/25 20:10:10  brouard
 int imx;    *** empty log message ***
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
 int estepm;    Author: Brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.154  2014/06/20 17:32:08  brouard
 int m,nb;    Summary: Outputs now all graphs of convergence to period prevalence
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.153  2014/06/20 16:45:46  brouard
 double **pmmij, ***probs, ***mobaverage;    Summary: If 3 live state, convergence to period prevalence on same graph
 double dateintmean=0;    Author: Brouard
   
 double *weight;    Revision 1.152  2014/06/18 17:54:09  brouard
 int **s; /* Status */    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.151  2014/06/18 16:43:30  brouard
     *** empty log message ***
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.150  2014/06/18 16:42:35  brouard
     Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 /**************** split *************************/    Author: brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.149  2014/06/18 15:51:14  brouard
    char *s;                             /* pointer */    Summary: Some fixes in parameter files errors
    int  l1, l2;                         /* length counters */    Author: Nicolas Brouard
   
    l1 = strlen( path );                 /* length of path */    Revision 1.148  2014/06/17 17:38:48  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Summary: Nothing new
 #ifdef windows    Author: Brouard
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Just a new packaging for OS/X version 0.98nS
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.147  2014/06/16 10:33:11  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    *** empty log message ***
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.146  2014/06/16 10:20:28  brouard
     Summary: Merge
       if ( getwd( dirc ) == NULL ) {    Author: Brouard
 #else  
       extern char       *getcwd( );    Merge, before building revised version.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.145  2014/06/10 21:23:15  brouard
 #endif    Summary: Debugging with valgrind
          return( GLOCK_ERROR_GETCWD );    Author: Nicolas Brouard
       }  
       strcpy( name, path );             /* we've got it */    Lot of changes in order to output the results with some covariates
    } else {                             /* strip direcotry from path */    After the Edimburgh REVES conference 2014, it seems mandatory to
       s++;                              /* after this, the filename */    improve the code.
       l2 = strlen( s );                 /* length of filename */    No more memory valgrind error but a lot has to be done in order to
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    continue the work of splitting the code into subroutines.
       strcpy( name, s );                /* save file name */    Also, decodemodel has been improved. Tricode is still not
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    optimal. nbcode should be improved. Documentation has been added in
       dirc[l1-l2] = 0;                  /* add zero */    the source code.
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.143  2014/01/26 09:45:38  brouard
 #ifdef windows    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #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; }    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.142  2014/01/26 03:57:36  brouard
    s++;    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.141  2014/01/26 02:42:01  brouard
    finame[l1-l2]= 0;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    return( 0 );                         /* we're done */  
 }    Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
   
 /******************************************/    Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 void replace(char *s, char*t)    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 {  
   int i;    Revision 1.138  2010/04/30 18:19:40  brouard
   int lg=20;    *** empty log message ***
   i=0;  
   lg=strlen(t);    Revision 1.137  2010/04/29 18:11:38  brouard
   for(i=0; i<= lg; i++) {    (Module): Checking covariates for more complex models
     (s[i] = t[i]);    than V1+V2. A lot of change to be done. Unstable.
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.136  2010/04/26 20:30:53  brouard
 }    (Module): merging some libgsl code. Fixing computation
     of likelione (using inter/intrapolation if mle = 0) in order to
 int nbocc(char *s, char occ)    get same likelihood as if mle=1.
 {    Some cleaning of code and comments added.
   int i,j=0;  
   int lg=20;    Revision 1.135  2009/10/29 15:33:14  brouard
   i=0;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.134  2009/10/29 13:18:53  brouard
   if  (s[i] == occ ) j++;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   }  
   return j;    Revision 1.133  2009/07/06 10:21:25  brouard
 }    just nforces
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.132  2009/07/06 08:22:05  brouard
 {    Many tings
   int i,lg,j,p=0;  
   i=0;    Revision 1.131  2009/06/20 16:22:47  brouard
   for(j=0; j<=strlen(t)-1; j++) {    Some dimensions resccaled
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
   lg=strlen(t);    lot of cleaning with variables initialized to 0. Trying to make
   for(j=0; j<p; j++) {    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
     (u[j] = t[j]);  
   }    Revision 1.129  2007/08/31 13:49:27  lievre
      u[p]='\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<= lg; j++) {    Revision 1.128  2006/06/30 13:02:05  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    (Module): Clarifications on computing e.j
   }  
 }    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 /********************** nrerror ********************/    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 void nrerror(char error_text[])    (Module): In order to speed up (in case of numerous covariates) we
 {    compute health expectancies (without variances) in a first step
   fprintf(stderr,"ERREUR ...\n");    and then all the health expectancies with variances or standard
   fprintf(stderr,"%s\n",error_text);    deviation (needs data from the Hessian matrices) which slows the
   exit(1);    computation.
 }    In the future we should be able to stop the program is only health
 /*********************** vector *******************/    expectancies and graph are needed without standard deviations.
 double *vector(int nl, int nh)  
 {    Revision 1.126  2006/04/28 17:23:28  brouard
   double *v;    (Module): Yes the sum of survivors was wrong since
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    imach-114 because nhstepm was no more computed in the age
   if (!v) nrerror("allocation failure in vector");    loop. Now we define nhstepma in the age loop.
   return v-nl+NR_END;    Version 0.98h
 }  
     Revision 1.125  2006/04/04 15:20:31  lievre
 /************************ free vector ******************/    Errors in calculation of health expectancies. Age was not initialized.
 void free_vector(double*v, int nl, int nh)    Forecasting file added.
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.124  2006/03/22 17:13:53  lievre
 }    Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.123  2006/03/20 10:52:43  brouard
 {    * imach.c (Module): <title> changed, corresponds to .htm file
   int *v;    name. <head> headers where missing.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    * imach.c (Module): Weights can have a decimal point as for
   return 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
 /******************free ivector **************************/    1.
 void free_ivector(int *v, long nl, long nh)    Version 0.98g
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.122  2006/03/20 09:45:41  brouard
 }    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 /******************* imatrix *******************************/    otherwise the weight is truncated).
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Modification of warning when the covariates values are not 0 or
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    1.
 {    Version 0.98g
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.121  2006/03/16 17:45:01  lievre
      * imach.c (Module): Comments concerning covariates added
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    * imach.c (Module): refinements in the computation of lli if
   if (!m) nrerror("allocation failure 1 in matrix()");    status=-2 in order to have more reliable computation if stepm is
   m += NR_END;    not 1 month. Version 0.98f
   m -= nrl;  
      Revision 1.120  2006/03/16 15:10:38  lievre
      (Module): refinements in the computation of lli if
   /* allocate rows and set pointers to them */    status=-2 in order to have more reliable computation if stepm is
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    not 1 month. Version 0.98f
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.119  2006/03/15 17:42:26  brouard
   m[nrl] -= ncl;    (Module): Bug if status = -2, the loglikelihood was
      computed as likelihood omitting the logarithm. Version O.98e
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      Revision 1.118  2006/03/14 18:20:07  brouard
   /* return pointer to array of pointers to rows */    (Module): varevsij Comments added explaining the second
   return m;    table of variances if popbased=1 .
 }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 /****************** free_imatrix *************************/    (Module): Version 0.98d
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.117  2006/03/14 17:16:22  brouard
       long nch,ncl,nrh,nrl;    (Module): varevsij Comments added explaining the second
      /* free an int matrix allocated by imatrix() */    table of variances if popbased=1 .
 {    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    (Module): Function pstamp added
   free((FREE_ARG) (m+nrl-NR_END));    (Module): Version 0.98d
 }  
     Revision 1.116  2006/03/06 10:29:27  brouard
 /******************* matrix *******************************/    (Module): Variance-covariance wrong links and
 double **matrix(long nrl, long nrh, long ncl, long nch)    varian-covariance of ej. is needed (Saito).
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Revision 1.115  2006/02/27 12:17:45  brouard
   double **m;    (Module): One freematrix added in mlikeli! 0.98c
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.114  2006/02/26 12:57:58  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Some improvements in processing parameter
   m += NR_END;    filename with strsep.
   m -= nrl;  
     Revision 1.113  2006/02/24 14:20:24  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Memory leaks checks with valgrind and:
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    datafile was not closed, some imatrix were not freed and on matrix
   m[nrl] += NR_END;    allocation too.
   m[nrl] -= ncl;  
     Revision 1.112  2006/01/30 09:55:26  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   return m;  
 }    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 /*************************free matrix ************************/    (Module): Comments can be added in data file. Missing date values
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    can be a simple dot '.'.
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.110  2006/01/25 00:51:50  brouard
   free((FREE_ARG)(m+nrl-NR_END));    (Module): Lots of cleaning and bugs added (Gompertz)
 }  
     Revision 1.109  2006/01/24 19:37:15  brouard
 /******************* ma3x *******************************/    (Module): Comments (lines starting with a #) are allowed in data.
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    Revision 1.108  2006/01/19 18:05:42  lievre
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Gnuplot problem appeared...
   double ***m;    To be fixed
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.107  2006/01/19 16:20:37  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    Test existence of gnuplot in imach path
   m += NR_END;  
   m -= nrl;    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.105  2006/01/05 20:23:19  lievre
   m[nrl] += NR_END;    *** empty log message ***
   m[nrl] -= ncl;  
     Revision 1.104  2005/09/30 16:11:43  lievre
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    that the person is alive, then we can code his/her status as -2
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    (instead of missing=-1 in earlier versions) and his/her
   m[nrl][ncl] += NR_END;    contributions to the likelihood is 1 - Prob of dying from last
   m[nrl][ncl] -= nll;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   for (j=ncl+1; j<=nch; j++)    the healthy state at last known wave). Version is 0.98
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Revision 1.103  2005/09/30 15:54:49  lievre
   for (i=nrl+1; i<=nrh; i++) {    (Module): sump fixed, loop imx fixed, and simplifications.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.102  2004/09/15 17:31:30  brouard
       m[i][j]=m[i][j-1]+nlay;    Add the possibility to read data file including tab characters.
   }  
   return m;    Revision 1.101  2004/09/15 10:38:38  brouard
 }    Fix on curr_time
   
 /*************************free ma3x ************************/    Revision 1.100  2004/07/12 18:29:06  brouard
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Add version for Mac OS X. Just define UNIX in Makefile
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Revision 1.99  2004/06/05 08:57:40  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    *** empty log message ***
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
 /***************** f1dim *************************/    directly from the data i.e. without the need of knowing the health
 extern int ncom;    state at each age, but using a Gompertz model: log u =a + b*age .
 extern double *pcom,*xicom;    This is the basic analysis of mortality and should be done before any
 extern double (*nrfunc)(double []);    other analysis, in order to test if the mortality estimated from the
      cross-longitudinal survey is different from the mortality estimated
 double f1dim(double x)    from other sources like vital statistic data.
 {  
   int j;    The same imach parameter file can be used but the option for mle should be -3.
   double f;  
   double *xt;    Agnès, who wrote this part of the code, tried to keep most of the
      former routines in order to include the new code within the former code.
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    The output is very simple: only an estimate of the intercept and of
   f=(*nrfunc)(xt);    the slope with 95% confident intervals.
   free_vector(xt,1,ncom);  
   return f;    Current limitations:
 }    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 /*****************brent *************************/    B) There is no computation of Life Expectancy nor Life Table.
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {    Revision 1.97  2004/02/20 13:25:42  lievre
   int iter;    Version 0.96d. Population forecasting command line is (temporarily)
   double a,b,d,etemp;    suppressed.
   double fu,fv,fw,fx;  
   double ftemp;    Revision 1.96  2003/07/15 15:38:55  brouard
   double p,q,r,tol1,tol2,u,v,w,x,xm;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   double e=0.0;    rewritten within the same printf. Workaround: many printfs.
    
   a=(ax < cx ? ax : cx);    Revision 1.95  2003/07/08 07:54:34  brouard
   b=(ax > cx ? ax : cx);    * imach.c (Repository):
   x=w=v=bx;    (Repository): Using imachwizard code to output a more meaningful covariance
   fw=fv=fx=(*f)(x);    matrix (cov(a12,c31) instead of numbers.
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    Revision 1.94  2003/06/27 13:00:02  brouard
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    Just cleaning
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    Revision 1.93  2003/06/25 16:33:55  brouard
 #ifdef DEBUG    (Module): On windows (cygwin) function asctime_r doesn't
     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);    exist so I changed back to asctime which exists.
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    (Module): Version 0.96b
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    Revision 1.92  2003/06/25 16:30:45  brouard
       *xmin=x;    (Module): On windows (cygwin) function asctime_r doesn't
       return fx;    exist so I changed back to asctime which exists.
     }  
     ftemp=fu;    Revision 1.91  2003/06/25 15:30:29  brouard
     if (fabs(e) > tol1) {    * imach.c (Repository): Duplicated warning errors corrected.
       r=(x-w)*(fx-fv);    (Repository): Elapsed time after each iteration is now output. It
       q=(x-v)*(fx-fw);    helps to forecast when convergence will be reached. Elapsed time
       p=(x-v)*q-(x-w)*r;    is stamped in powell.  We created a new html file for the graphs
       q=2.0*(q-r);    concerning matrix of covariance. It has extension -cov.htm.
       if (q > 0.0) p = -p;  
       q=fabs(q);    Revision 1.90  2003/06/24 12:34:15  brouard
       etemp=e;    (Module): Some bugs corrected for windows. Also, when
       e=d;    mle=-1 a template is output in file "or"mypar.txt with the design
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    of the covariance matrix to be input.
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {    Revision 1.89  2003/06/24 12:30:52  brouard
         d=p/q;    (Module): Some bugs corrected for windows. Also, when
         u=x+d;    mle=-1 a template is output in file "or"mypar.txt with the design
         if (u-a < tol2 || b-u < tol2)    of the covariance matrix to be input.
           d=SIGN(tol1,xm-x);  
       }    Revision 1.88  2003/06/23 17:54:56  brouard
     } else {    * 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.
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }    Revision 1.87  2003/06/18 12:26:01  brouard
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    Version 0.96
     fu=(*f)(u);  
     if (fu <= fx) {    Revision 1.86  2003/06/17 20:04:08  brouard
       if (u >= x) a=x; else b=x;    (Module): Change position of html and gnuplot routines and added
       SHFT(v,w,x,u)    routine fileappend.
         SHFT(fv,fw,fx,fu)  
         } else {    Revision 1.85  2003/06/17 13:12:43  brouard
           if (u < x) a=u; else b=u;    * imach.c (Repository): Check when date of death was earlier that
           if (fu <= fw || w == x) {    current date of interview. It may happen when the death was just
             v=w;    prior to the death. In this case, dh was negative and likelihood
             w=u;    was wrong (infinity). We still send an "Error" but patch by
             fv=fw;    assuming that the date of death was just one stepm after the
             fw=fu;    interview.
           } else if (fu <= fv || v == x || v == w) {    (Repository): Because some people have very long ID (first column)
             v=u;    we changed int to long in num[] and we added a new lvector for
             fv=fu;    memory allocation. But we also truncated to 8 characters (left
           }    truncation)
         }    (Repository): No more line truncation errors.
   }  
   nrerror("Too many iterations in brent");    Revision 1.84  2003/06/13 21:44:43  brouard
   *xmin=x;    * imach.c (Repository): Replace "freqsummary" at a correct
   return fx;    place. It differs from routine "prevalence" which may be called
 }    many times. Probs is memory consuming and must be used with
     parcimony.
 /****************** mnbrak ***********************/    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Revision 1.83  2003/06/10 13:39:11  lievre
             double (*func)(double))    *** empty log message ***
 {  
   double ulim,u,r,q, dum;    Revision 1.82  2003/06/05 15:57:20  brouard
   double fu;    Add log in  imach.c and  fullversion number is now printed.
    
   *fa=(*func)(*ax);  */
   *fb=(*func)(*bx);  /*
   if (*fb > *fa) {     Interpolated Markov Chain
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)    Short summary of the programme:
       }    
   *cx=(*bx)+GOLD*(*bx-*ax);    This program computes Healthy Life Expectancies from
   *fc=(*func)(*cx);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   while (*fb > *fc) {    first survey ("cross") where individuals from different ages are
     r=(*bx-*ax)*(*fb-*fc);    interviewed on their health status or degree of disability (in the
     q=(*bx-*cx)*(*fb-*fa);    case of a health survey which is our main interest) -2- at least a
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    second wave of interviews ("longitudinal") which measure each change
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    (if any) in individual health status.  Health expectancies are
     ulim=(*bx)+GLIMIT*(*cx-*bx);    computed from the time spent in each health state according to a
     if ((*bx-u)*(u-*cx) > 0.0) {    model. More health states you consider, more time is necessary to reach the
       fu=(*func)(u);    Maximum Likelihood of the parameters involved in the model.  The
     } else if ((*cx-u)*(u-ulim) > 0.0) {    simplest model is the multinomial logistic model where pij is the
       fu=(*func)(u);    probability to be observed in state j at the second wave
       if (fu < *fc) {    conditional to be observed in state i at the first wave. Therefore
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
           SHFT(*fb,*fc,fu,(*func)(u))    'age' is age and 'sex' is a covariate. If you want to have a more
           }    complex model than "constant and age", you should modify the program
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    where the markup *Covariates have to be included here again* invites
       u=ulim;    you to do it.  More covariates you add, slower the
       fu=(*func)(u);    convergence.
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);    The advantage of this computer programme, compared to a simple
       fu=(*func)(u);    multinomial logistic model, is clear when the delay between waves is not
     }    identical for each individual. Also, if a individual missed an
     SHFT(*ax,*bx,*cx,u)    intermediate interview, the information is lost, but taken into
       SHFT(*fa,*fb,*fc,fu)    account using an interpolation or extrapolation.  
       }  
 }    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
 /*************** linmin ************************/    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 int ncom;    semester or year) is modelled as a multinomial logistic.  The hPx
 double *pcom,*xicom;    matrix is simply the matrix product of nh*stepm elementary matrices
 double (*nrfunc)(double []);    and the contribution of each individual to the likelihood is simply
      hPijx.
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {    Also this programme outputs the covariance matrix of the parameters but also
   double brent(double ax, double bx, double cx,    of the life expectancies. It also computes the period (stable) prevalence. 
                double (*f)(double), double tol, double *xmin);    
   double f1dim(double x);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,             Institut national d'études démographiques, Paris.
               double *fc, double (*func)(double));    This software have been partly granted by Euro-REVES, a concerted action
   int j;    from the European Union.
   double xx,xmin,bx,ax;    It is copyrighted identically to a GNU software product, ie programme and
   double fx,fb,fa;    software can be distributed freely for non commercial use. Latest version
      can be accessed at http://euroreves.ined.fr/imach .
   ncom=n;  
   pcom=vector(1,n);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   xicom=vector(1,n);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   nrfunc=func;    
   for (j=1;j<=n;j++) {    **********************************************************************/
     pcom[j]=p[j];  /*
     xicom[j]=xi[j];    main
   }    read parameterfile
   ax=0.0;    read datafile
   xx=1.0;    concatwav
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    freqsummary
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    if (mle >= 1)
 #ifdef DEBUG      mlikeli
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    print results files
 #endif    if mle==1 
   for (j=1;j<=n;j++) {       computes hessian
     xi[j] *= xmin;    read end of parameter file: agemin, agemax, bage, fage, estepm
     p[j] += xi[j];        begin-prev-date,...
   }    open gnuplot file
   free_vector(xicom,1,n);    open html file
   free_vector(pcom,1,n);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 }     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
                                     | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 /*************** powell ************************/      freexexit2 possible for memory heap.
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))    h Pij x                         | pij_nom  ficrestpij
 {     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   void linmin(double p[], double xi[], int n, double *fret,         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
               double (*func)(double []));         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   double fp,fptt;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   double *xits;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   pt=vector(1,n);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   ptt=vector(1,n);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   xit=vector(1,n);  
   xits=vector(1,n);    forecasting if prevfcast==1 prevforecast call prevalence()
   *fret=(*func)(p);    health expectancies
   for (j=1;j<=n;j++) pt[j]=p[j];    Variance-covariance of DFLE
   for (*iter=1;;++(*iter)) {    prevalence()
     fp=(*fret);     movingaverage()
     ibig=0;    varevsij() 
     del=0.0;    if popbased==1 varevsij(,popbased)
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    total life expectancies
     for (i=1;i<=n;i++)    Variance of period (stable) prevalence
       printf(" %d %.12f",i, p[i]);   end
     printf("\n");  */
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /* #define DEBUG */
       fptt=(*fret);  /* #define DEBUGBRENT */
 #ifdef DEBUG  #define POWELL /* Instead of NLOPT */
       printf("fret=%lf \n",*fret);  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
 #endif  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  #include <math.h>
       if (fabs(fptt-(*fret)) > del) {  #include <stdio.h>
         del=fabs(fptt-(*fret));  #include <stdlib.h>
         ibig=i;  #include <string.h>
       }  
 #ifdef DEBUG  #ifdef _WIN32
       printf("%d %.12e",i,(*fret));  #include <io.h>
       for (j=1;j<=n;j++) {  #include <windows.h>
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #include <tchar.h>
         printf(" x(%d)=%.12e",j,xit[j]);  #else
       }  #include <unistd.h>
       for(j=1;j<=n;j++)  #endif
         printf(" p=%.12e",p[j]);  
       printf("\n");  #include <limits.h>
 #endif  #include <sys/types.h>
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #if defined(__GNUC__)
 #ifdef DEBUG  #include <sys/utsname.h> /* Doesn't work on Windows */
       int k[2],l;  #endif
       k[0]=1;  
       k[1]=-1;  #include <sys/stat.h>
       printf("Max: %.12e",(*func)(p));  #include <errno.h>
       for (j=1;j<=n;j++)  /* extern int errno; */
         printf(" %.12e",p[j]);  
       printf("\n");  /* #ifdef LINUX */
       for(l=0;l<=1;l++) {  /* #include <time.h> */
         for (j=1;j<=n;j++) {  /* #include "timeval.h" */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /* #else */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  /* #include <sys/time.h> */
         }  /* #endif */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  #include <time.h>
 #endif  
   #ifdef GSL
   #include <gsl/gsl_errno.h>
       free_vector(xit,1,n);  #include <gsl/gsl_multimin.h>
       free_vector(xits,1,n);  #endif
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  
       return;  #ifdef NLOPT
     }  #include <nlopt.h>
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  typedef struct {
     for (j=1;j<=n;j++) {    double (* function)(double [] );
       ptt[j]=2.0*p[j]-pt[j];  } myfunc_data ;
       xit[j]=p[j]-pt[j];  #endif
       pt[j]=p[j];  
     }  /* #include <libintl.h> */
     fptt=(*func)(ptt);  /* #define _(String) gettext (String) */
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  #define GNUPLOTPROGRAM "gnuplot"
         for (j=1;j<=n;j++) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
           xi[j][ibig]=xi[j][n];  #define FILENAMELENGTH 132
           xi[j][n]=xit[j];  
         }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #ifdef DEBUG  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
           printf(" %.12e",xit[j]);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
         printf("\n");  
 #endif  #define NINTERVMAX 8
       }  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     }  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   }  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 }  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   #define MAXN 20000
 /**** Prevalence limit ****************/  #define YEARM 12. /**< Number of months per year */
   #define AGESUP 130
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #define AGEBASE 40
 {  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #ifdef _WIN32
      matrix by transitions matrix until convergence is reached */  #define DIRSEPARATOR '\\'
   #define CHARSEPARATOR "\\"
   int i, ii,j,k;  #define ODIRSEPARATOR '/'
   double min, max, maxmin, maxmax,sumnew=0.;  #else
   double **matprod2();  #define DIRSEPARATOR '/'
   double **out, cov[NCOVMAX], **pmij();  #define CHARSEPARATOR "/"
   double **newm;  #define ODIRSEPARATOR '\\'
   double agefin, delaymax=50 ; /* Max number of years to converge */  #endif
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  /* $Id$ */
     for (j=1;j<=nlstate+ndeath;j++){  /* $State$ */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  char version[]="Imach version 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
   char fullversion[]="$Revision$ $Date$"; 
    cov[1]=1.;  char strstart[80];
    char optionfilext[10], optionfilefiname[FILENAMELENGTH];
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
     newm=savm;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
     /* Covariates have to be included here again */  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
      cov[2]=agefin;  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
    int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       for (k=1; k<=cptcovn;k++) {  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int cptcovprodnoage=0; /**< Number of covariate products without age */   
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       }  int cptcov=0; /* Working variable */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int npar=NPARMAX;
       for (k=1; k<=cptcovprod;k++)  int nlstate=2; /* Number of live states */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  int ndeath=1; /* Number of dead states */
   int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int popbased=0;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  int *wav; /* Number of waves for this individuual 0 is possible */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  int maxwav=0; /* Maxim number of waves */
   int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     savm=oldm;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     oldm=newm;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     maxmax=0.;                     to the likelihood and the sum of weights (done by funcone)*/
     for(j=1;j<=nlstate;j++){  int mle=1, weightopt=0;
       min=1.;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       max=0.;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       for(i=1; i<=nlstate; i++) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         sumnew=0;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  int countcallfunc=0;  /* Count the number of calls to func */
         prlim[i][j]= newm[i][j]/(1-sumnew);  double jmean=1; /* Mean space between 2 waves */
         max=FMAX(max,prlim[i][j]);  double **matprod2(); /* test */
         min=FMIN(min,prlim[i][j]);  double **oldm, **newm, **savm; /* Working pointers to matrices */
       }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       maxmin=max-min;  /*FILE *fic ; */ /* Used in readdata only */
       maxmax=FMAX(maxmax,maxmin);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     }  FILE *ficlog, *ficrespow;
     if(maxmax < ftolpl){  int globpr=0; /* Global variable for printing or not */
       return prlim;  double fretone; /* Only one call to likelihood */
     }  long ipmx=0; /* Number of contributions */
   }  double sw; /* Sum of weights */
 }  char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 /*************** transition probabilities ***************/  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  FILE *ficresprobmorprev;
 {  FILE *fichtm, *fichtmcov; /* Html File */
   double s1, s2;  FILE *ficreseij;
   /*double t34;*/  char filerese[FILENAMELENGTH];
   int i,j,j1, nc, ii, jj;  FILE *ficresstdeij;
   char fileresstde[FILENAMELENGTH];
     for(i=1; i<= nlstate; i++){  FILE *ficrescveij;
     for(j=1; j<i;j++){  char filerescve[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  FILE  *ficresvij;
         /*s2 += param[i][j][nc]*cov[nc];*/  char fileresv[FILENAMELENGTH];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  FILE  *ficresvpl;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  char fileresvpl[FILENAMELENGTH];
       }  char title[MAXLINE];
       ps[i][j]=s2;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     for(j=i+1; j<=nlstate+ndeath;j++){  char command[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int  outcmd=0;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       }  
       ps[i][j]=s2;  char filelog[FILENAMELENGTH]; /* Log file */
     }  char filerest[FILENAMELENGTH];
   }  char fileregp[FILENAMELENGTH];
     /*ps[3][2]=1;*/  char popfile[FILENAMELENGTH];
   
   for(i=1; i<= nlstate; i++){  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
      s1=0;  
     for(j=1; j<i; j++)  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       s1+=exp(ps[i][j]);  /* struct timezone tzp; */
     for(j=i+1; j<=nlstate+ndeath; j++)  /* extern int gettimeofday(); */
       s1+=exp(ps[i][j]);  struct tm tml, *gmtime(), *localtime();
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  extern time_t time();
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  struct tm tm;
   } /* end i */  
   char strcurr[80], strfor[80];
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  char *endptr;
       ps[ii][jj]=0;  long lval;
       ps[ii][ii]=1;  double dval;
     }  
   }  #define NR_END 1
   #define FREE_ARG char*
   #define FTOL 1.0e-10
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  #define NRANSI 
      printf("%lf ",ps[ii][jj]);  #define ITMAX 200 
    }  
     printf("\n ");  #define TOL 2.0e-4 
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  #define CGOLD 0.3819660 
 /*  #define ZEPS 1.0e-10 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   goto end;*/  
     return ps;  #define GOLD 1.618034 
 }  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 /**************** Product of 2 matrices ******************/  
   static double maxarg1,maxarg2;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   /* in, b, out are matrice of pointers which should have been initialized  #define rint(a) floor(a+0.5)
      before: only the contents of out is modified. The function returns  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
      a pointer to pointers identical to out */  #define mytinydouble 1.0e-16
   long i, j, k;  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   for(i=nrl; i<= nrh; i++)  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
     for(k=ncolol; k<=ncoloh; k++)  /* static double dsqrarg; */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
         out[i][k] +=in[i][j]*b[j][k];  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   return out;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  int agegomp= AGEGOMP;
   
   int imx; 
 /************* Higher Matrix Product ***************/  int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  int estepm;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  int m,nb;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  long *num;
      (typically every 2 years instead of every month which is too big).  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
      Model is determined by parameters x and covariates have to be  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
      included manually here.  double **pmmij, ***probs;
   double *ageexmed,*agecens;
      */  double dateintmean=0;
   
   int i, j, d, h, k;  double *weight;
   double **out, cov[NCOVMAX];  int **s; /* Status */
   double **newm;  double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   /* Hstepm could be zero and should return the unit matrix */                    * covar=matrix(0,NCOVMAX,1,n); 
   for (i=1;i<=nlstate+ndeath;i++)                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
     for (j=1;j<=nlstate+ndeath;j++){  double  idx; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  int *Ndum; /** Freq of modality (tricode */
     }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   for(h=1; h <=nhstepm; h++){  double *lsurv, *lpop, *tpop;
     for(d=1; d <=hstepm; d++){  
       newm=savm;  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
       /* Covariates have to be included here again */  double ftolhess; /**< Tolerance for computing hessian */
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /**************** split *************************/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       for (k=1; k<=cptcovprod;k++)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    */ 
     char  *ss;                            /* pointer */
     int   l1=0, l2=0;                             /* length counters */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    l1 = strlen(path );                   /* length of path */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       savm=oldm;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       oldm=newm;      strcpy( name, path );               /* we got the fullname name because no directory */
     }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     for(i=1; i<=nlstate+ndeath; i++)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       for(j=1;j<=nlstate+ndeath;j++) {      /* get current working directory */
         po[i][j][h]=newm[i][j];      /*    extern  char* getcwd ( char *buf , int len);*/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  #ifdef WIN32
          */      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
       }  #else
   } /* end h */          if (getcwd(dirc, FILENAME_MAX) == NULL) {
   return po;  #endif
 }        return( GLOCK_ERROR_GETCWD );
       }
       /* got dirc from getcwd*/
 /*************** log-likelihood *************/      printf(" DIRC = %s \n",dirc);
 double func( double *x)    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   int i, ii, j, k, mi, d, kk;      l2 = strlen( ss );                  /* length of filename */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   double **out;      strcpy( name, ss );         /* save file name */
   double sw; /* Sum of weights */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   double lli; /* Individual log likelihood */      dirc[l1-l2] = '\0';                 /* add zero */
   long ipmx;      printf(" DIRC2 = %s \n",dirc);
   /*extern weight */    }
   /* We are differentiating ll according to initial status */    /* We add a separator at the end of dirc if not exists */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    l1 = strlen( dirc );                  /* length of directory */
   /*for(i=1;i<imx;i++)    if( dirc[l1-1] != DIRSEPARATOR ){
     printf(" %d\n",s[4][i]);      dirc[l1] =  DIRSEPARATOR;
   */      dirc[l1+1] = 0; 
   cov[1]=1.;      printf(" DIRC3 = %s \n",dirc);
     }
   for(k=1; k<=nlstate; k++) ll[k]=0.;    ss = strrchr( name, '.' );            /* find last / */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    if (ss >0){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      ss++;
     for(mi=1; mi<= wav[i]-1; mi++){      strcpy(ext,ss);                     /* save extension */
       for (ii=1;ii<=nlstate+ndeath;ii++)      l1= strlen( name);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      l2= strlen(ss)+1;
       for(d=0; d<dh[mi][i]; d++){      strncpy( finame, name, l1-l2);
         newm=savm;      finame[l1-l2]= 0;
         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];    return( 0 );                          /* we're done */
         }  }
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /******************************************/
         savm=oldm;  
         oldm=newm;  void replace_back_to_slash(char *s, char*t)
          {
            int i;
       } /* end mult */    int lg=0;
          i=0;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    lg=strlen(t);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    for(i=0; i<= lg; i++) {
       ipmx +=1;      (s[i] = t[i]);
       sw += weight[i];      if (t[i]== '\\') s[i]='/';
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    }
     } /* end of wave */  }
   } /* end of individual */  
   char *trimbb(char *out, char *in)
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    char *s;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    s=out;
   return -l;    while (*in != '\0'){
 }      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         in++;
       }
 /*********** Maximum Likelihood Estimation ***************/      *out++ = *in++;
     }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    *out='\0';
 {    return s;
   int i,j, iter;  }
   double **xi,*delti;  
   double fret;  /* char *substrchaine(char *out, char *in, char *chain) */
   xi=matrix(1,npar,1,npar);  /* { */
   for (i=1;i<=npar;i++)  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
     for (j=1;j<=npar;j++)  /*   char *s, *t; */
       xi[i][j]=(i==j ? 1.0 : 0.0);  /*   t=in;s=out; */
   printf("Powell\n");  /*   while ((*in != *chain) && (*in != '\0')){ */
   powell(p,xi,npar,ftol,&iter,&fret,func);  /*     *out++ = *in++; */
   /*   } */
    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));  /*   /\* *in matches *chain *\/ */
   /*   while ((*in++ == *chain++) && (*in != '\0')){ */
 }  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*   } */
 /**** Computes Hessian and covariance matrix ***/  /*   in--; chain--; */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*   while ( (*in != '\0')){ */
 {  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   double  **a,**y,*x,pd;  /*     *out++ = *in++; */
   double **hess;  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   int i, j,jk;  /*   } */
   int *indx;  /*   *out='\0'; */
   /*   out=s; */
   double hessii(double p[], double delta, int theta, double delti[]);  /*   return out; */
   double hessij(double p[], double delti[], int i, int j);  /* } */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  char *substrchaine(char *out, char *in, char *chain)
   void ludcmp(double **a, int npar, int *indx, double *d) ;  {
     /* Substract chain 'chain' from 'in', return and output 'out' */
   hess=matrix(1,npar,1,npar);    /* in="V1+V1*age+age*age+V2", chain="age*age" */
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    char *strloc;
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);    strcpy (out, in); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
     /*printf(" %f ",p[i]);*/    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
     /*printf(" %lf ",hess[i][i]);*/    if(strloc != NULL){ 
   }      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
        memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
   for (i=1;i<=npar;i++) {      /* strcpy (strloc, strloc +strlen(chain));*/
     for (j=1;j<=npar;j++)  {    }
       if (j>i) {    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
         printf(".%d%d",i,j);fflush(stdout);    return out;
         hess[i][j]=hessij(p,delti,i,j);  }
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  
       }  char *cutl(char *blocc, char *alocc, char *in, char occ)
     }  {
   }    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
   printf("\n");       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef" and alocc="ghi2j".
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       If occ is not found blocc is null and alocc is equal to in. Returns blocc
      */
   a=matrix(1,npar,1,npar);    char *s, *t;
   y=matrix(1,npar,1,npar);    t=in;s=in;
   x=vector(1,npar);    while ((*in != occ) && (*in != '\0')){
   indx=ivector(1,npar);      *alocc++ = *in++;
   for (i=1;i<=npar;i++)    }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    if( *in == occ){
   ludcmp(a,npar,indx,&pd);      *(alocc)='\0';
       s=++in;
   for (j=1;j<=npar;j++) {    }
     for (i=1;i<=npar;i++) x[i]=0;   
     x[j]=1;    if (s == t) {/* occ not found */
     lubksb(a,npar,indx,x);      *(alocc-(in-s))='\0';
     for (i=1;i<=npar;i++){      in=s;
       matcov[i][j]=x[i];    }
     }    while ( *in != '\0'){
   }      *blocc++ = *in++;
     }
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {    *blocc='\0';
     for (j=1;j<=npar;j++) {    return t;
       printf("%.3e ",hess[i][j]);  }
     }  char *cutv(char *blocc, char *alocc, char *in, char occ)
     printf("\n");  {
   }    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
        and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   /* Recompute Inverse */       gives blocc="abcdef2ghi" and alocc="j".
   for (i=1;i<=npar;i++)       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    */
   ludcmp(a,npar,indx,&pd);    char *s, *t;
     t=in;s=in;
   /*  printf("\n#Hessian matrix recomputed#\n");    while (*in != '\0'){
       while( *in == occ){
   for (j=1;j<=npar;j++) {        *blocc++ = *in++;
     for (i=1;i<=npar;i++) x[i]=0;        s=in;
     x[j]=1;      }
     lubksb(a,npar,indx,x);      *blocc++ = *in++;
     for (i=1;i<=npar;i++){    }
       y[i][j]=x[i];    if (s == t) /* occ not found */
       printf("%.3e ",y[i][j]);      *(blocc-(in-s))='\0';
     }    else
     printf("\n");      *(blocc-(in-s)-1)='\0';
   }    in=s;
   */    while ( *in != '\0'){
       *alocc++ = *in++;
   free_matrix(a,1,npar,1,npar);    }
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);    *alocc='\0';
   free_ivector(indx,1,npar);    return s;
   free_matrix(hess,1,npar,1,npar);  }
   
   int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /*************** hessian matrix ****************/    int lg=20;
 double hessii( double x[], double delta, int theta, double delti[])    i=0;
 {    lg=strlen(s);
   int i;    for(i=0; i<= lg; i++) {
   int l=1, lmax=20;    if  (s[i] == occ ) j++;
   double k1,k2;    }
   double p2[NPARMAX+1];    return j;
   double res;  }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;  /* void cutv(char *u,char *v, char*t, char occ) */
   int k=0,kmax=10;  /* { */
   double l1;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   fx=func(x);  /*      gives u="abcdef2ghi" and v="j" *\/ */
   for (i=1;i<=npar;i++) p2[i]=x[i];  /*   int i,lg,j,p=0; */
   for(l=0 ; l <=lmax; l++){  /*   i=0; */
     l1=pow(10,l);  /*   lg=strlen(t); */
     delts=delt;  /*   for(j=0; j<=lg-1; j++) { */
     for(k=1 ; k <kmax; k=k+1){  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       delt = delta*(l1*k);  /*   } */
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  /*   for(j=0; j<p; j++) { */
       p2[theta]=x[theta]-delt;  /*     (u[j] = t[j]); */
       k2=func(p2)-fx;  /*   } */
       /*res= (k1-2.0*fx+k2)/delt/delt; */  /*      u[p]='\0'; */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
        /*    for(j=0; j<= lg; j++) { */
 #ifdef DEBUG  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       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  /* } */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  #ifdef _WIN32
         k=kmax;  char * strsep(char **pp, const char *delim)
       }  {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    char *p, *q;
         k=kmax; l=lmax*10.;           
       }    if ((p = *pp) == NULL)
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      return 0;
         delts=delt;    if ((q = strpbrk (p, delim)) != NULL)
       }    {
     }      *pp = q + 1;
   }      *q = '\0';
   delti[theta]=delts;    }
   return res;    else
        *pp = 0;
 }    return p;
   }
 double hessij( double x[], double delti[], int thetai,int thetaj)  #endif
 {  
   int i;  /********************** nrerror ********************/
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;  void nrerror(char error_text[])
   double p2[NPARMAX+1];  {
   int k;    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
   fx=func(x);    exit(EXIT_FAILURE);
   for (k=1; k<=2; k++) {  }
     for (i=1;i<=npar;i++) p2[i]=x[i];  /*********************** vector *******************/
     p2[thetai]=x[thetai]+delti[thetai]/k;  double *vector(int nl, int nh)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  {
     k1=func(p2)-fx;    double *v;
      v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     p2[thetai]=x[thetai]+delti[thetai]/k;    if (!v) nrerror("allocation failure in vector");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    return v-nl+NR_END;
     k2=func(p2)-fx;  }
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /************************ free vector ******************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  void free_vector(double*v, int nl, int nh)
     k3=func(p2)-fx;  {
      free((FREE_ARG)(v+nl-NR_END));
     p2[thetai]=x[thetai]-delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;  /************************ivector *******************************/
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  int *ivector(long nl,long nh)
 #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);    int *v;
 #endif    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   }    if (!v) nrerror("allocation failure in ivector");
   return res;    return v-nl+NR_END;
 }  }
   
 /************** Inverse of matrix **************/  /******************free ivector **************************/
 void ludcmp(double **a, int n, int *indx, double *d)  void free_ivector(int *v, long nl, long nh)
 {  {
   int i,imax,j,k;    free((FREE_ARG)(v+nl-NR_END));
   double big,dum,sum,temp;  }
   double *vv;  
    /************************lvector *******************************/
   vv=vector(1,n);  long *lvector(long nl,long nh)
   *d=1.0;  {
   for (i=1;i<=n;i++) {    long *v;
     big=0.0;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     for (j=1;j<=n;j++)    if (!v) nrerror("allocation failure in ivector");
       if ((temp=fabs(a[i][j])) > big) big=temp;    return v-nl+NR_END;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  }
     vv[i]=1.0/big;  
   }  /******************free lvector **************************/
   for (j=1;j<=n;j++) {  void free_lvector(long *v, long nl, long nh)
     for (i=1;i<j;i++) {  {
       sum=a[i][j];    free((FREE_ARG)(v+nl-NR_END));
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  }
       a[i][j]=sum;  
     }  /******************* imatrix *******************************/
     big=0.0;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     for (i=j;i<=n;i++) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       sum=a[i][j];  { 
       for (k=1;k<j;k++)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         sum -= a[i][k]*a[k][j];    int **m; 
       a[i][j]=sum;    
       if ( (dum=vv[i]*fabs(sum)) >= big) {    /* allocate pointers to rows */ 
         big=dum;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         imax=i;    if (!m) nrerror("allocation failure 1 in matrix()"); 
       }    m += NR_END; 
     }    m -= nrl; 
     if (j != imax) {    
       for (k=1;k<=n;k++) {    
         dum=a[imax][k];    /* allocate rows and set pointers to them */ 
         a[imax][k]=a[j][k];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         a[j][k]=dum;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       }    m[nrl] += NR_END; 
       *d = -(*d);    m[nrl] -= ncl; 
       vv[imax]=vv[j];    
     }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     indx[j]=imax;    
     if (a[j][j] == 0.0) a[j][j]=TINY;    /* return pointer to array of pointers to rows */ 
     if (j != n) {    return m; 
       dum=1.0/(a[j][j]);  } 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  /****************** free_imatrix *************************/
   }  void free_imatrix(m,nrl,nrh,ncl,nch)
   free_vector(vv,1,n);  /* Doesn't work */        int **m;
 ;        long nch,ncl,nrh,nrl; 
 }       /* free an int matrix allocated by imatrix() */ 
   { 
 void lubksb(double **a, int n, int *indx, double b[])    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 {    free((FREE_ARG) (m+nrl-NR_END)); 
   int i,ii=0,ip,j;  } 
   double sum;  
    /******************* matrix *******************************/
   for (i=1;i<=n;i++) {  double **matrix(long nrl, long nrh, long ncl, long nch)
     ip=indx[i];  {
     sum=b[ip];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     b[ip]=b[i];    double **m;
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     else if (sum) ii=i;    if (!m) nrerror("allocation failure 1 in matrix()");
     b[i]=sum;    m += NR_END;
   }    m -= nrl;
   for (i=n;i>=1;i--) {  
     sum=b[i];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     b[i]=sum/a[i][i];    m[nrl] += NR_END;
   }    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /************ Frequencies ********************/    return m;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
 {  /* Some frequencies */  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
    that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;     */
   double ***freq; /* Frequencies */  }
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  /*************************free matrix ************************/
   FILE *ficresp;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   char fileresp[FILENAMELENGTH];  {
      free((FREE_ARG)(m[nrl]+ncl-NR_END));
   pp=vector(1,nlstate);    free((FREE_ARG)(m+nrl-NR_END));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);  /******************* ma3x *******************************/
   if((ficresp=fopen(fileresp,"w"))==NULL) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     printf("Problem with prevalence resultfile: %s\n", fileresp);  {
     exit(0);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   }    double ***m;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      if (!m) nrerror("allocation failure 1 in matrix()");
   j=cptcoveff;    m += NR_END;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    m -= nrl;
    
   for(k1=1; k1<=j;k1++){    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for(i1=1; i1<=ncodemax[k1];i1++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       j1++;    m[nrl] += NR_END;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    m[nrl] -= ncl;
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)      for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
             freq[i][jk][m]=0;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
          m[nrl][ncl] += NR_END;
       dateintsum=0;    m[nrl][ncl] -= nll;
       k2cpt=0;    for (j=ncl+1; j<=nch; j++) 
       for (i=1; i<=imx; i++) {      m[nrl][j]=m[nrl][j-1]+nlay;
         bool=1;    
         if  (cptcovn>0) {    for (i=nrl+1; i<=nrh; i++) {
           for (z1=1; z1<=cptcoveff; z1++)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for (j=ncl+1; j<=nch; j++) 
               bool=0;        m[i][j]=m[i][j-1]+nlay;
         }    }
         if (bool==1) {    return m; 
           for(m=firstpass; m<=lastpass; m++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
             k2=anint[m][i]+(mint[m][i]/12.);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    */
               if(agev[m][i]==0) agev[m][i]=agemax+1;  }
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {  /*************************free ma3x ************************/
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  {
               }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
                  free((FREE_ARG)(m[nrl]+ncl-NR_END));
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    free((FREE_ARG)(m+nrl-NR_END));
                 dateintsum=dateintsum+k2;  }
                 k2cpt++;  
               }  /*************** function subdirf ***********/
             }  char *subdirf(char fileres[])
           }  {
         }    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
            strcat(tmpout,"/"); /* Add to the right */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    strcat(tmpout,fileres);
     return tmpout;
       if  (cptcovn>0) {  }
         fprintf(ficresp, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /*************** function subdirf2 ***********/
         fprintf(ficresp, "**********\n#");  char *subdirf2(char fileres[], char *preop)
       }  {
       for(i=1; i<=nlstate;i++)    
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    /* Caution optionfilefiname is hidden */
       fprintf(ficresp, "\n");    strcpy(tmpout,optionfilefiname);
          strcat(tmpout,"/");
       for(i=(int)agemin; i <= (int)agemax+3; i++){    strcat(tmpout,preop);
         if(i==(int)agemax+3)    strcat(tmpout,fileres);
           printf("Total");    return tmpout;
         else  }
           printf("Age %d", i);  
         for(jk=1; jk <=nlstate ; jk++){  /*************** function subdirf3 ***********/
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  char *subdirf3(char fileres[], char *preop, char *preop2)
             pp[jk] += freq[jk][m][i];  {
         }    
         for(jk=1; jk <=nlstate ; jk++){    /* Caution optionfilefiname is hidden */
           for(m=-1, pos=0; m <=0 ; m++)    strcpy(tmpout,optionfilefiname);
             pos += freq[jk][m][i];    strcat(tmpout,"/");
           if(pp[jk]>=1.e-10)    strcat(tmpout,preop);
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    strcat(tmpout,preop2);
           else    strcat(tmpout,fileres);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    return tmpout;
         }  }
   
         for(jk=1; jk <=nlstate ; jk++){  char *asc_diff_time(long time_sec, char ascdiff[])
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  {
             pp[jk] += freq[jk][m][i];    long sec_left, days, hours, minutes;
         }    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
         for(jk=1,pos=0; jk <=nlstate ; jk++)    hours = (sec_left) / (60*60) ;
           pos += pp[jk];    sec_left = (sec_left) %(60*60);
         for(jk=1; jk <=nlstate ; jk++){    minutes = (sec_left) /60;
           if(pos>=1.e-5)    sec_left = (sec_left) % (60);
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
           else    return ascdiff;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  }
           if( i <= (int) agemax){  
             if(pos>=1.e-5){  /***************** f1dim *************************/
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  extern int ncom; 
               probs[i][jk][j1]= pp[jk]/pos;  extern double *pcom,*xicom;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  extern double (*nrfunc)(double []); 
             }   
             else  double f1dim(double x) 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  { 
           }    int j; 
         }    double f;
            double *xt; 
         for(jk=-1; jk <=nlstate+ndeath; jk++)   
           for(m=-1; m <=nlstate+ndeath; m++)    xt=vector(1,ncom); 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         if(i <= (int) agemax)    f=(*nrfunc)(xt); 
           fprintf(ficresp,"\n");    free_vector(xt,1,ncom); 
         printf("\n");    return f; 
       }  } 
     }  
   }  /*****************brent *************************/
   dateintmean=dateintsum/k2cpt;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
    {
   fclose(ficresp);    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
   free_vector(pp,1,nlstate);     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
       * the minimum is returned as xmin, and the minimum function value is returned as brent , the
   /* End of Freq */     * returned function value. 
 }    */
     int iter; 
 /************ Prevalence ********************/    double a,b,d,etemp;
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    double fu=0,fv,fw,fx;
 {  /* Some frequencies */    double ftemp=0.;
      double p,q,r,tol1,tol2,u,v,w,x,xm; 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    double e=0.0; 
   double ***freq; /* Frequencies */   
   double *pp;    a=(ax < cx ? ax : cx); 
   double pos, k2;    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
   pp=vector(1,nlstate);    fw=fv=fx=(*f)(x); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (iter=1;iter<=ITMAX;iter++) { 
        xm=0.5*(a+b); 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   j1=0;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
        printf(".");fflush(stdout);
   j=cptcoveff;      fprintf(ficlog,".");fflush(ficlog);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  #ifdef DEBUGBRENT
        printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   for(k1=1; k1<=j;k1++){      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(i1=1; i1<=ncodemax[k1];i1++){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       j1++;  #endif
            if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       for (i=-1; i<=nlstate+ndeath; i++)          *xmin=x; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          return fx; 
           for(m=agemin; m <= agemax+3; m++)      } 
             freq[i][jk][m]=0;      ftemp=fu;
            if (fabs(e) > tol1) { 
       for (i=1; i<=imx; i++) {        r=(x-w)*(fx-fv); 
         bool=1;        q=(x-v)*(fx-fw); 
         if  (cptcovn>0) {        p=(x-v)*q-(x-w)*r; 
           for (z1=1; z1<=cptcoveff; z1++)        q=2.0*(q-r); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        if (q > 0.0) p = -p; 
               bool=0;        q=fabs(q); 
         }        etemp=e; 
         if (bool==1) {        e=d; 
           for(m=firstpass; m<=lastpass; m++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
             k2=anint[m][i]+(mint[m][i]/12.);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        else { 
               if(agev[m][i]==0) agev[m][i]=agemax+1;          d=p/q; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;          u=x+d; 
               if (m<lastpass) {          if (u-a < tol2 || b-u < tol2) 
                 if (calagedate>0)            d=SIGN(tol1,xm-x); 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        } 
                 else      } else { 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      } 
               }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
             }      fu=(*f)(u); 
           }      if (fu <= fx) { 
         }        if (u >= x) a=x; else b=x; 
       }        SHFT(v,w,x,u) 
       for(i=(int)agemin; i <= (int)agemax+3; i++){        SHFT(fv,fw,fx,fu) 
         for(jk=1; jk <=nlstate ; jk++){      } else { 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        if (u < x) a=u; else b=u; 
             pp[jk] += freq[jk][m][i];        if (fu <= fw || w == x) { 
         }          v=w; 
         for(jk=1; jk <=nlstate ; jk++){          w=u; 
           for(m=-1, pos=0; m <=0 ; m++)          fv=fw; 
             pos += freq[jk][m][i];          fw=fu; 
         }        } else if (fu <= fv || v == x || v == w) { 
                  v=u; 
         for(jk=1; jk <=nlstate ; jk++){          fv=fu; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } 
             pp[jk] += freq[jk][m][i];      } 
         }    } 
            nrerror("Too many iterations in brent"); 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    *xmin=x; 
            return fx; 
         for(jk=1; jk <=nlstate ; jk++){      } 
           if( i <= (int) agemax){  
             if(pos>=1.e-5){  /****************** mnbrak ***********************/
               probs[i][jk][j1]= pp[jk]/pos;  
             }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           }              double (*func)(double)) 
         }  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
          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
     }  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
   }     */
     double ulim,u,r,q, dum;
      double fu; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);    double scale=10.;
      int iterscale=0;
 }  /* End of Freq */  
     *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
 /************* Waves Concatenation ***************/    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
      Death is a valid wave (if date is known).    /*   *bx = *ax - (*ax - *bx)/scale; */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    /* } */
      and mw[mi+1][i]. dh depends on stepm.  
      */    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
   int i, mi, m;      SHFT(dum,*fb,*fa,dum) 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    } 
      double sum=0., jmean=0.;*/    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
   int j, k=0,jk, ju, jl;  #ifdef DEBUG
   double sum=0.;    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
   jmin=1e+5;    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
   jmax=-1;  #endif
   jmean=0.;    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
   for(i=1; i<=imx; i++){      r=(*bx-*ax)*(*fb-*fc); 
     mi=0;      q=(*bx-*cx)*(*fb-*fa); 
     m=firstpass;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     while(s[m][i] <= nlstate){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
       if(s[m][i]>=1)      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
         mw[++mi][i]=m;      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
       if(m >=lastpass)        fu=(*func)(u); 
         break;  #ifdef DEBUG
       else        /* f(x)=A(x-u)**2+f(u) */
         m++;        double A, fparabu; 
     }/* end while */        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
     if (s[m][i] > nlstate){        fparabu= *fa - A*(*ax-u)*(*ax-u);
       mi++;     /* Death is another wave */        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
       /* if(mi==0)  never been interviewed correctly before death */        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);
          /* Only death is a correct wave */        /* And thus,it can be that fu > *fc even if fparabu < *fc */
       mw[mi][i]=m;        /* 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) */
         /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
     wav[i]=mi;  #endif 
     if(mi==0)  #ifdef MNBRAKORIGINAL
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  #else
   }        if (fu > *fc) {
   #ifdef DEBUG
   for(i=1; i<=imx; i++){        printf("mnbrak4  fu > fc \n");
     for(mi=1; mi<wav[i];mi++){        fprintf(ficlog, "mnbrak4 fu > fc\n");
       if (stepm <=0)  #endif
         dh[mi][i]=1;          /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/  */
       else{          /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
         if (s[mw[mi+1][i]][i] > nlstate) {          dum=u; /* Shifting c and u */
           if (agedc[i] < 2*AGESUP) {          u = *cx;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          *cx = dum;
           if(j==0) j=1;  /* Survives at least one month after exam */          dum = fu;
           k=k+1;          fu = *fc;
           if (j >= jmax) jmax=j;          *fc =dum;
           if (j <= jmin) jmin=j;        } else { /* end */
           sum=sum+j;  #ifdef DEBUG
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        printf("mnbrak3  fu < fc \n");
           }        fprintf(ficlog, "mnbrak3 fu < fc\n");
         }  #endif
         else{          dum=u; /* Shifting c and u */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          u = *cx;
           k=k+1;          *cx = dum;
           if (j >= jmax) jmax=j;          dum = fu;
           else if (j <= jmin)jmin=j;          fu = *fc;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          *fc =dum;
           sum=sum+j;        }
         }  #endif
         jk= j/stepm;      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
         jl= j -jk*stepm;  #ifdef DEBUG
         ju= j -(jk+1)*stepm;        printf("mnbrak2  u after c but before ulim\n");
         if(jl <= -ju)        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
           dh[mi][i]=jk;  #endif
         else        fu=(*func)(u); 
           dh[mi][i]=jk+1;        if (fu < *fc) { 
         if(dh[mi][i]==0)  #ifdef DEBUG
           dh[mi][i]=1; /* At least one step */        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");
     }  #endif
   }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   jmean=sum/k;          SHFT(*fb,*fc,fu,(*func)(u)) 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        } 
  }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
 /*********** Tricode ****************************/  #ifdef DEBUG
 void tricode(int *Tvar, int **nbcode, int imx)        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
 {        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
   int Ndum[20],ij=1, k, j, i;  #endif
   int cptcode=0;        u=ulim; 
   cptcoveff=0;        fu=(*func)(u); 
        } else { /* u could be left to b (if r > q parabola has a maximum) */
   for (k=0; k<19; k++) Ndum[k]=0;  #ifdef DEBUG
   for (k=1; k<=7; k++) ncodemax[k]=0;        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
         fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  #endif
     for (i=1; i<=imx; i++) {        u=(*cx)+GOLD*(*cx-*bx); 
       ij=(int)(covar[Tvar[j]][i]);        fu=(*func)(u); 
       Ndum[ij]++;      } /* end tests */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      SHFT(*ax,*bx,*cx,u) 
       if (ij > cptcode) cptcode=ij;      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);
     for (i=0; i<=cptcode; i++) {        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(Ndum[i]!=0) ncodemax[j]++;  #endif
     }    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
     ij=1;  } 
   
   /*************** linmin ************************/
     for (i=1; i<=ncodemax[j]; i++) {  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
       for (k=0; k<=19; k++) {  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
         if (Ndum[k] != 0) {  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
           nbcode[Tvar[j]][ij]=k;  the value of func at the returned location p . This is actually all accomplished by calling the
            routines mnbrak and brent .*/
           ij++;  int ncom; 
         }  double *pcom,*xicom;
         if (ij > ncodemax[j]) break;  double (*nrfunc)(double []); 
       }     
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   }    { 
     double brent(double ax, double bx, double cx, 
  for (k=0; k<19; k++) Ndum[k]=0;                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
  for (i=1; i<=ncovmodel-2; i++) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       ij=Tvar[i];                double *fc, double (*func)(double)); 
       Ndum[ij]++;    int j; 
     }    double xx,xmin,bx,ax; 
     double fx,fb,fa;
  ij=1;  
  for (i=1; i<=10; i++) {    double scale=10., axs, xxs, xxss; /* Scale added for infinity */
    if((Ndum[i]!=0) && (i<=ncovcol)){   
      Tvaraff[ij]=i;    ncom=n; 
      ij++;    pcom=vector(1,n); 
    }    xicom=vector(1,n); 
  }    nrfunc=func; 
      for (j=1;j<=n;j++) { 
     cptcoveff=ij-1;      pcom[j]=p[j]; 
 }      xicom[j]=xi[j]; 
     } 
 /*********** Health Expectancies ****************/  
     axs=0.0;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )    xxss=1; /* 1 and using scale */
     xxs=1;
 {    do{
   /* Health expectancies */      ax=0.;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      xx= xxs;
   double age, agelim, hf;      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
   double ***p3mat,***varhe;      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
   double **dnewm,**doldm;      /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
   double *xp;      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
   double **gp, **gm;      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
   double ***gradg, ***trgradg;      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
   int theta;      /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
       if (fx != fx){
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
   xp=vector(1,npar);          printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
   dnewm=matrix(1,nlstate*2,1,npar);      }
   doldm=matrix(1,nlstate*2,1,nlstate*2);    }while(fx != fx);
    
   fprintf(ficreseij,"# Health expectancies\n");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
   fprintf(ficreseij,"# Age");    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
   for(i=1; i<=nlstate;i++)    /* fmin = f(p[j] + xmin * xi[j]) */
     for(j=1; j<=nlstate;j++)    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
   fprintf(ficreseij,"\n");  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   if(estepm < stepm){    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf ("Problem %d lower than %d\n",estepm, stepm);  #endif
   }    printf("linmin end ");
   else  hstepm=estepm;      for (j=1;j<=n;j++) { 
   /* We compute the life expectancy from trapezoids spaced every estepm months      printf(" before xi[%d]=%12.8f", j,xi[j]);
    * This is mainly to measure the difference between two models: for example      xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
    * if stepm=24 months pijx are given only every 2 years and by summing them      if(xxs <1.0)
    * we are calculating an estimate of the Life Expectancy assuming a linear        printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
    * progression inbetween and thus overestimating or underestimating according      p[j] += xi[j]; /* Parameters values are updated accordingly */
    * 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    printf("\n");
    * to compare the new estimate of Life expectancy with the same linear    free_vector(xicom,1,n); 
    * hypothesis. A more precise result, taking into account a more precise    free_vector(pcom,1,n); 
    * curvature will be obtained if estepm is as small as stepm. */  } 
   
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  /*************** powell ************************/
      nhstepm is the number of hstepm from age to agelim  /*
      nstepm is the number of stepm from age to agelin.  Minimization of a function func of n variables. Input consists of an initial starting point
      Look at hpijx to understand the reason of that which relies in memory size  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
      and note for a fixed period like estepm months */  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  such that failure to decrease by more than this amount on one iteration signals doneness. On
      survival function given by stepm (the optimization length). Unfortunately it  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
      means that if the survival funtion is printed only each two years of age and if  function value at p , and iter is the number of iterations taken. The routine linmin is used.
      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.  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   */              double (*func)(double [])) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   agelim=AGESUP;                double (*func)(double [])); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int i,ibig,j; 
     /* nhstepm age range expressed in number of stepm */    double del,t,*pt,*ptt,*xit;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    double directest;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    double fp,fptt;
     /* if (stepm >= YEARM) hstepm=1;*/    double *xits;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    int niterf, itmp;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    pt=vector(1,n); 
     gp=matrix(0,nhstepm,1,nlstate*2);    ptt=vector(1,n); 
     gm=matrix(0,nhstepm,1,nlstate*2);    xit=vector(1,n); 
     xits=vector(1,n); 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    *fret=(*func)(p); 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    for (j=1;j<=n;j++) pt[j]=p[j]; 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        rcurr_time = time(NULL);  
      for (*iter=1;;++(*iter)) { 
       fp=(*fret); /* From former iteration or initial value */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      ibig=0; 
       del=0.0; 
     /* Computing Variances of health expectancies */      rlast_time=rcurr_time;
       /* (void) gettimeofday(&curr_time,&tzp); */
      for(theta=1; theta <=npar; theta++){      rcurr_time = time(NULL);  
       for(i=1; i<=npar; i++){      curr_time = *localtime(&rcurr_time);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
       for (i=1;i<=n;i++) {
       cptj=0;        printf(" %d %.12f",i, p[i]);
       for(j=1; j<= nlstate; j++){        fprintf(ficlog," %d %.12lf",i, p[i]);
         for(i=1; i<=nlstate; i++){        fprintf(ficrespow," %.12lf", p[i]);
           cptj=cptj+1;      }
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      printf("\n");
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      fprintf(ficlog,"\n");
           }      fprintf(ficrespow,"\n");fflush(ficrespow);
         }      if(*iter <=3){
       }        tml = *localtime(&rcurr_time);
              strcpy(strcurr,asctime(&tml));
              rforecast_time=rcurr_time; 
       for(i=1; i<=npar; i++)        itmp = strlen(strcurr);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            strcurr[itmp-1]='\0';
              printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       cptj=0;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(j=1; j<= nlstate; j++){        for(niterf=10;niterf<=30;niterf+=10){
         for(i=1;i<=nlstate;i++){          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
           cptj=cptj+1;          forecast_time = *localtime(&rforecast_time);
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          strcpy(strfor,asctime(&forecast_time));
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          itmp = strlen(strfor);
           }          if(strfor[itmp-1]=='\n')
         }          strfor[itmp-1]='\0';
       }          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);
       for(j=1; j<= nlstate*2; j++)          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         for(h=0; h<=nhstepm-1; h++){        }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      }
         }      for (i=1;i<=n;i++) { /* For each direction i */
      }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
            fptt=(*fret); 
 /* End theta */  #ifdef DEBUG
             printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   #endif
      for(h=0; h<=nhstepm-1; h++)            printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       for(j=1; j<=nlstate*2;j++)        fprintf(ficlog,"%d",i);fflush(ficlog);
         for(theta=1; theta <=npar; theta++)        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input. Outputs are fret(new point p) p is updated and xit rescaled */
           trgradg[h][j][theta]=gradg[h][theta][j];        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
                                               because that direction will be replaced unless the gain del is small
                                         in comparison with the 'probable' gain, mu^2, with the last average direction.
      for(i=1;i<=nlstate*2;i++)                                        Unless the n directions are conjugate some gain in the determinant may be obtained
       for(j=1;j<=nlstate*2;j++)                                        with the new direction.
         varhe[i][j][(int)age] =0.;                                        */
           del=fabs(fptt-(*fret)); 
      printf("%d|",(int)age);fflush(stdout);          ibig=i; 
      for(h=0;h<=nhstepm-1;h++){        } 
       for(k=0;k<=nhstepm-1;k++){  #ifdef DEBUG
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        printf("%d %.12e",i,(*fret));
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        fprintf(ficlog,"%d %.12e",i,(*fret));
         for(i=1;i<=nlstate*2;i++)        for (j=1;j<=n;j++) {
           for(j=1;j<=nlstate*2;j++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          printf(" x(%d)=%.12e",j,xit[j]);
       }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     }        }
         for(j=1;j<=n;j++) {
                printf(" p(%d)=%.12e",j,p[j]);
     /* Computing expectancies */          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++)        printf("\n");
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        fprintf(ficlog,"\n");
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  #endif
                } /* end loop on each direction i */
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
       /* But p and xit have been updated at the end of linmin and do not produce *fret any more! */
         }      /* New value of last point Pn is not computed, P(n-1) */
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
     fprintf(ficreseij,"%3.0f",age );  #ifdef DEBUG
     cptj=0;        int k[2],l;
     for(i=1; i<=nlstate;i++)        k[0]=1;
       for(j=1; j<=nlstate;j++){        k[1]=-1;
         cptj++;        printf("Max: %.12e",(*func)(p));
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        fprintf(ficlog,"Max: %.12e",(*func)(p));
       }        for (j=1;j<=n;j++) {
     fprintf(ficreseij,"\n");          printf(" %.12e",p[j]);
              fprintf(ficlog," %.12e",p[j]);
     free_matrix(gm,0,nhstepm,1,nlstate*2);        }
     free_matrix(gp,0,nhstepm,1,nlstate*2);        printf("\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        fprintf(ficlog,"\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        for(l=0;l<=1;l++) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (j=1;j<=n;j++) {
   }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   free_vector(xp,1,npar);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   free_matrix(dnewm,1,nlstate*2,1,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]);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          }
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          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)));
         }
 /************ Variance ******************/  #endif
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)  
 {  
   /* Variance of health expectancies */        free_vector(xit,1,n); 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        free_vector(xits,1,n); 
   double **newm;        free_vector(ptt,1,n); 
   double **dnewm,**doldm;        free_vector(pt,1,n); 
   int i, j, nhstepm, hstepm, h, nstepm ;        return; 
   int k, cptcode;      } 
   double *xp;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double **gp, **gm;      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
   double ***gradg, ***trgradg;        ptt[j]=2.0*p[j]-pt[j]; 
   double ***p3mat;        xit[j]=p[j]-pt[j]; 
   double age,agelim, hf;        pt[j]=p[j]; 
   int theta;      } 
       fptt=(*func)(ptt); /* f_3 */
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   fprintf(ficresvij,"# Age");        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
   for(i=1; i<=nlstate;i++)        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
     for(j=1; j<=nlstate;j++)        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   fprintf(ficresvij,"\n");        /* 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 */
   xp=vector(1,npar);        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   dnewm=matrix(1,nlstate,1,npar);  #ifdef NRCORIGINAL
   doldm=matrix(1,nlstate,1,nlstate);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
    #else
   if(estepm < stepm){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
     printf ("Problem %d lower than %d\n",estepm, stepm);        t= t- del*SQR(fp-fptt);
   }  #endif
   else  hstepm=estepm;          directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
   /* For example we decided to compute the life expectancy with the smallest unit */  #ifdef DEBUG
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        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);
      nhstepm is the number of hstepm from age to agelim        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);
      nstepm is the number of stepm from age to agelin.        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
      Look at hpijx to understand the reason of that which relies in memory size               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
      and note for a fixed period like k years */        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
      survival function given by stepm (the optimization length). Unfortunately it        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);
      means that if the survival funtion is printed only each two years of age and if        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);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  #endif
      results. So we changed our mind and took the option of the best precision.  #ifdef POWELLORIGINAL
   */        if (t < 0.0) { /* Then we use it for new direction */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  #else
   agelim = AGESUP;        if (directest*t < 0.0) { /* Contradiction between both tests */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        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=ma3x(0,nhstepm,1,npar,1,nlstate);      } 
     gp=matrix(0,nhstepm,1,nlstate);        if (directest < 0.0) { /* Then we use it for new direction */
     gm=matrix(0,nhstepm,1,nlstate);  #endif
           linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
     for(theta=1; theta <=npar; theta++){          for (j=1;j<=n;j++) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
       }          }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   
       if (popbased==1) {  #ifdef DEBUG
         for(i=1; i<=nlstate;i++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           prlim[i][i]=probs[(int)age][i][ij];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       }          for(j=1;j<=n;j++){
              printf(" %.12e",xit[j]);
       for(j=1; j<= nlstate; j++){            fprintf(ficlog," %.12e",xit[j]);
         for(h=0; h<=nhstepm; h++){          }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          printf("\n");
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          fprintf(ficlog,"\n");
         }  #endif
       }        } /* end of t negative */
          } /* end if (fptt < fp)  */
       for(i=1; i<=npar; i++) /* Computes gradient */    } 
         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);  /**** Prevalence limit (stable or period prevalence)  ****************/
    
       if (popbased==1) {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         for(i=1; i<=nlstate;i++)  {
           prlim[i][i]=probs[(int)age][i][ij];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
     
       for(j=1; j<= nlstate; j++){    int i, ii,j,k;
         for(h=0; h<=nhstepm; h++){    double min, max, maxmin, maxmax,sumnew=0.;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    /* double **matprod2(); */ /* test */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double **out, cov[NCOVMAX+1], **pmij();
         }    double **newm;
       }    double agefin, delaymax=50 ; /* Max number of years to converge */
     
       for(j=1; j<= nlstate; j++)    for (ii=1;ii<=nlstate+ndeath;ii++)
         for(h=0; h<=nhstepm; h++){      for (j=1;j<=nlstate+ndeath;j++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }      }
     } /* End theta */    
     cov[1]=1.;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=0; h<=nhstepm; h++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       for(j=1; j<=nlstate;j++)      newm=savm;
         for(theta=1; theta <=npar; theta++)      /* Covariates have to be included here again */
           trgradg[h][j][theta]=gradg[h][theta][j];      cov[2]=agefin;
       if(nagesqr==1)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        cov[3]= agefin*agefin;;
     for(i=1;i<=nlstate;i++)      for (k=1; k<=cptcovn;k++) {
       for(j=1;j<=nlstate;j++)        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         vareij[i][j][(int)age] =0.;        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
       }
     for(h=0;h<=nhstepm;h++){      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(k=0;k<=nhstepm;k++){      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for (k=1; k<=cptcovprod;k++) /* Useless */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         for(i=1;i<=nlstate;i++)      
           for(j=1;j<=nlstate;j++)      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       }      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     }      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
     fprintf(ficresvij,"%.0f ",age );      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
     for(i=1; i<=nlstate;i++)      
       for(j=1; j<=nlstate;j++){      savm=oldm;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      oldm=newm;
       }      maxmax=0.;
     fprintf(ficresvij,"\n");      for(j=1;j<=nlstate;j++){
     free_matrix(gp,0,nhstepm,1,nlstate);        min=1.;
     free_matrix(gm,0,nhstepm,1,nlstate);        max=0.;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for(i=1; i<=nlstate; i++) {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          sumnew=0;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   } /* End age */          prlim[i][j]= newm[i][j]/(1-sumnew);
            /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
   free_vector(xp,1,npar);          max=FMAX(max,prlim[i][j]);
   free_matrix(doldm,1,nlstate,1,npar);          min=FMIN(min,prlim[i][j]);
   free_matrix(dnewm,1,nlstate,1,nlstate);        }
         maxmin=max-min;
 }        maxmax=FMAX(maxmax,maxmin);
       } /* j loop */
 /************ Variance of prevlim ******************/      if(maxmax < ftolpl){
 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)        return prlim;
 {      }
   /* Variance of prevalence limit */    } /* age loop */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    return prlim; /* should not reach here */
   double **newm;  }
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;  /*************** transition probabilities ***************/ 
   int k, cptcode;  
   double *xp;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   double *gp, *gm;  {
   double **gradg, **trgradg;    /* According to parameters values stored in x and the covariate's values stored in cov,
   double age,agelim;       computes the probability to be observed in state j being in state i by appying the
   int theta;       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]
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   fprintf(ficresvpl,"# Age");       ncth covariate in the global vector x is given by the formula:
   for(i=1; i<=nlstate;i++)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
       fprintf(ficresvpl," %1d-%1d",i,i);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   fprintf(ficresvpl,"\n");       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   xp=vector(1,npar);       Outputs ps[i][j] the probability to be observed in j being in j according to
   dnewm=matrix(1,nlstate,1,npar);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   doldm=matrix(1,nlstate,1,nlstate);    */
      double s1, lnpijopii;
   hstepm=1*YEARM; /* Every year of age */    /*double t34;*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    int i,j, nc, ii, jj;
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for(i=1; i<= nlstate; i++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(j=1; j<i;j++){
     if (stepm >= YEARM) hstepm=1;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     gradg=matrix(1,npar,1,nlstate);            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     gp=vector(1,nlstate);  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     gm=vector(1,nlstate);          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     for(theta=1; theta <=npar; theta++){  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       for(i=1; i<=npar; i++){ /* Computes gradient */        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(j=i+1; j<=nlstate+ndeath;j++){
       }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
       for(i=1;i<=nlstate;i++)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
         gp[i] = prlim[i][i];  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
              }
       for(i=1; i<=npar; i++) /* Computes gradient */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         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++){
         s1=0;
       for(i=1;i<=nlstate;i++)        for(j=1; j<i; j++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     } /* End theta */          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
     trgradg =matrix(1,nlstate,1,npar);        for(j=i+1; j<=nlstate+ndeath; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     for(j=1; j<=nlstate;j++)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       for(theta=1; theta <=npar; theta++)        }
         trgradg[j][theta]=gradg[theta][j];        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         ps[i][i]=1./(s1+1.);
     for(i=1;i<=nlstate;i++)        /* Computing other pijs */
       varpl[i][(int)age] =0.;        for(j=1; j<i; j++)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          ps[i][j]= exp(ps[i][j])*ps[i][i];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        for(j=i+1; j<=nlstate+ndeath; j++)
     for(i=1;i<=nlstate;i++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
     fprintf(ficresvpl,"%.0f ",age );      
     for(i=1; i<=nlstate;i++)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        for(jj=1; jj<= nlstate+ndeath; jj++){
     fprintf(ficresvpl,"\n");          ps[ii][jj]=0;
     free_vector(gp,1,nlstate);          ps[ii][ii]=1;
     free_vector(gm,1,nlstate);        }
     free_matrix(gradg,1,npar,1,nlstate);      }
     free_matrix(trgradg,1,nlstate,1,npar);      
   } /* End age */      
       /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   free_vector(xp,1,npar);      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   free_matrix(doldm,1,nlstate,1,npar);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   free_matrix(dnewm,1,nlstate,1,nlstate);      /*   } */
       /*   printf("\n "); */
 }      /* } */
       /* printf("\n ");printf("%lf ",cov[2]);*/
 /************ Variance of one-step probabilities  ******************/      /*
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
 {        goto end;*/
   int i, j, i1, k1, j1, z1;      return ps;
   int k=0,l, cptcode;  }
   double **dnewm,**doldm;  
   double *xp;  /**************** Product of 2 matrices ******************/
   double *gp, *gm;  
   double **gradg, **trgradg;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   double age,agelim, cov[NCOVMAX];  {
   int theta;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   char fileresprob[FILENAMELENGTH];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   char fileresprobcov[FILENAMELENGTH];    /* in, b, out are matrice of pointers which should have been initialized 
   char fileresprobcor[FILENAMELENGTH];       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
   strcpy(fileresprob,"prob");    int i, j, k;
   strcat(fileresprob,fileres);    for(i=nrl; i<= nrh; i++)
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      for(k=ncolol; k<=ncoloh; k++){
     printf("Problem with resultfile: %s\n", fileresprob);        out[i][k]=0.;
   }        for(j=ncl; j<=nch; j++)
   strcpy(fileresprobcov,"probcov");          out[i][k] +=in[i][j]*b[j][k];
   strcat(fileresprobcov,fileres);      }
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    return out;
     printf("Problem with resultfile: %s\n", fileresprobcov);  }
   }  
   strcpy(fileresprobcor,"probcor");  
   strcat(fileresprobcor,fileres);  /************* Higher Matrix Product ***************/
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcor);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   }  {
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    /* Computes the transition matrix starting at age 'age' over 
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);       'nhstepm*hstepm*stepm' months (i.e. until
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         nhstepm*hstepm matrices. 
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   fprintf(ficresprob,"# Age");       (typically every 2 years instead of every month which is too big 
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");       for the memory).
   fprintf(ficresprobcov,"# Age");       Model is determined by parameters x and covariates have to be 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");       included manually here. 
   fprintf(ficresprobcov,"# Age");  
   for(i=1; i<=nlstate;i++)       */
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    int i, j, d, h, k;
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    double **out, cov[NCOVMAX+1];
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    double **newm;
     }      double agexact;
   fprintf(ficresprob,"\n");  
   fprintf(ficresprobcov,"\n");    /* Hstepm could be zero and should return the unit matrix */
   fprintf(ficresprobcor,"\n");    for (i=1;i<=nlstate+ndeath;i++)
   xp=vector(1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        po[i][j][0]=(i==j ? 1.0 : 0.0);
        }
   cov[1]=1;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   j=cptcoveff;    for(h=1; h <=nhstepm; h++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for(d=1; d <=hstepm; d++){
   j1=0;        newm=savm;
   for(k1=1; k1<=1;k1++){        /* Covariates have to be included here again */
     for(i1=1; i1<=ncodemax[k1];i1++){        cov[1]=1.;
     j1++;        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         cov[2]=agexact;
     if  (cptcovn>0) {        if(nagesqr==1)
       fprintf(ficresprob, "\n#********** Variable ");          cov[3]= agexact*agexact;
       fprintf(ficresprobcov, "\n#********** Variable ");        for (k=1; k<=cptcovn;k++) 
       fprintf(ficresprobcor, "\n#********** Variable ");          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
       fprintf(ficresprob, "**********\n#");          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
       fprintf(ficresprobcov, "**********\n#");        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       fprintf(ficresprobcor, "**********\n#");  
     }  
            /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       for (age=bage; age<=fage; age ++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         cov[2]=age;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         for (k=1; k<=cptcovn;k++) {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        savm=oldm;
         }        oldm=newm;
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      }
         for (k=1; k<=cptcovprod;k++)      for(i=1; i<=nlstate+ndeath; i++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        for(j=1;j<=nlstate+ndeath;j++) {
                  po[i][j][h]=newm[i][j];
         gradg=matrix(1,npar,1,9);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         trgradg=matrix(1,9,1,npar);        }
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      /*printf("h=%d ",h);*/
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    } /* end h */
      /*     printf("\n H=%d \n",h); */
         for(theta=1; theta <=npar; theta++){    return po;
           for(i=1; i<=npar; i++)  }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  
            #ifdef NLOPT
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
              double fret;
           k=0;    double *xt;
           for(i=1; i<= (nlstate+ndeath); i++){    int j;
             for(j=1; j<=(nlstate+ndeath);j++){    myfunc_data *d2 = (myfunc_data *) pd;
               k=k+1;  /* xt = (p1-1); */
               gp[k]=pmmij[i][j];    xt=vector(1,n); 
             }    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
           }  
              fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
           for(i=1; i<=npar; i++)    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    printf("Function = %.12lf ",fret);
        for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    printf("\n");
           k=0;   free_vector(xt,1,n);
           for(i=1; i<=(nlstate+ndeath); i++){    return fret;
             for(j=1; j<=(nlstate+ndeath);j++){  }
               k=k+1;  #endif
               gm[k]=pmmij[i][j];  
             }  /*************** log-likelihood *************/
           }  double func( double *x)
        {
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    int i, ii, j, k, mi, d, kk;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         }    double **out;
     double sw; /* Sum of weights */
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    double lli; /* Individual log likelihood */
           for(theta=1; theta <=npar; theta++)    int s1, s2;
             trgradg[j][theta]=gradg[theta][j];    double bbh, survp;
            long ipmx;
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    double agexact;
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    /*extern weight */
            /* We are differentiating ll according to initial status */
         pmij(pmmij,cov,ncovmodel,x,nlstate);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
            /*for(i=1;i<imx;i++) 
         k=0;      printf(" %d\n",s[4][i]);
         for(i=1; i<=(nlstate+ndeath); i++){    */
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;    ++countcallfunc;
             gm[k]=pmmij[i][j];  
           }    cov[1]=1.;
         }  
          for(k=1; k<=nlstate; k++) ll[k]=0.;
         /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    if(mle==1){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      }*/        /* Computes the values of the ncovmodel covariates of the model
            depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
         fprintf(ficresprob,"\n%d ",(int)age);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
         fprintf(ficresprobcov,"\n%d ",(int)age);           to be observed in j being in i according to the model.
         fprintf(ficresprobcor,"\n%d ",(int)age);         */
         for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)            cov[2+nagesqr+k]=covar[Tvar[k]][i];
           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));        }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
           fprintf(ficresprobcov,"%12.3e ",gm[i]);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
           fprintf(ficresprobcor,"%12.3e ",gm[i]);           has been calculated etc */
         }        for(mi=1; mi<= wav[i]-1; mi++){
         i=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
         for (k=1; k<=(nlstate);k++){            for (j=1;j<=nlstate+ndeath;j++){
           for (l=1; l<=(nlstate+ndeath);l++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             i=i++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);            }
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);          for(d=0; d<dh[mi][i]; d++){
             for (j=1; j<=i;j++){            newm=savm;
               fprintf(ficresprobcov," %12.3e",doldm[i][j]);            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));            cov[2]=agexact;
             }            if(nagesqr==1)
           }              cov[3]= agexact*agexact;
         }            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
     }            }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            savm=oldm;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            oldm=newm;
   }          } /* end mult */
   free_vector(xp,1,npar);        
   fclose(ficresprob);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   fclose(ficresprobcov);          /* But now since version 0.9 we anticipate for bias at large stepm.
   fclose(ficresprobcor);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 }           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
 /******************* Printing html file ***********/           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \           * probability in order to take into account the bias as a fraction of the way
                   int lastpass, int stepm, int weightopt, char model[],\           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \           * -stepm/2 to stepm/2 .
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\           * For stepm=1 the results are the same as for previous versions of Imach.
                   char version[], int popforecast, int estepm ,\           * For stepm > 1 the results are less biased than in previous versions. 
                   double jprev1, double mprev1,double anprev1, \           */
                   double jprev2, double mprev2,double anprev2){          s1=s[mw[mi][i]][i];
   int jj1, k1, i1, cpt;          s2=s[mw[mi+1][i]][i];
   FILE *fichtm;          bbh=(double)bh[mi][i]/(double)stepm; 
   /*char optionfilehtm[FILENAMELENGTH];*/          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   strcpy(optionfilehtm,optionfile);           */
   strcat(optionfilehtm,".htm");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          if( s2 > nlstate){ 
     printf("Problem with %s \n",optionfilehtm), exit(0);            /* i.e. if s2 is a death state and if the date of death is known 
   }               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n               which is also equal to probability to die before dh 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n               minus probability to die before dh-stepm . 
 \n               In version up to 0.92 likelihood was computed
 Total number of observations=%d <br>\n          as if date of death was unknown. Death was treated as any other
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n          health state: the date of the interview describes the actual state
 <hr  size=\"2\" color=\"#EC5E5E\">          and not the date of a change in health state. The former idea was
  <ul><li>Parameter files<br>\n          to consider that at each interview the state was recorded
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          (healthy, disable or death) and IMaCh was corrected; but when we
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n          contribution is smaller and very dependent of the step unit
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n          stepm. It is no more the probability to die between last interview
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n          and month of death but the probability to survive from last
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n          interview up to one month before death multiplied by the
  - Life expectancies by age and initial health status (estepm=%2d months):          probability to die within a month. Thanks to Chris
    <a href=\"e%s\">e%s</a> <br>\n</li>", \          Jackson for correcting this bug.  Former versions increased
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n          lower mortality.
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n            */
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n          /* If, at the beginning of the maximization mostly, the
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n             cumulative probability or probability to be dead is
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n             constant (ie = 1) over time d, the difference is equal to
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n             0.  out[s1][3] = savm[s1][3]: probability, being at state
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n             s1 at precedent wave, to be dead a month before current
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);             wave is equal to probability, being at state s1 at
              precedent wave, to be dead at mont of the current
  if(popforecast==1) fprintf(fichtm,"\n             wave. Then the observed probability (that this person died)
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n             is null according to current estimated parameter. In fact,
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n             it should be very low but not zero otherwise the log go to
         <br>",fileres,fileres,fileres,fileres);             infinity.
  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);  /* #ifdef INFINITYORIGINAL */
 fprintf(fichtm," <li>Graphs</li><p>");  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #else */
  m=cptcoveff;  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  /*          lli=log(mytinydouble); */
   /*        else */
  jj1=0;  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
  for(k1=1; k1<=m;k1++){  /* #endif */
    for(i1=1; i1<=ncodemax[k1];i1++){              lli=log(out[s1][s2] - savm[s1][s2]);
      jj1++;  
      if (cptcovn > 0) {          } else if  (s2==-2) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            for (j=1,survp=0. ; j<=nlstate; j++) 
        for (cpt=1; cpt<=cptcoveff;cpt++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            /*survp += out[s1][j]; */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            lli= log(survp);
      }          }
      /* Pij */          
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>          else if  (s2==-4) { 
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                for (j=3,survp=0. ; j<=nlstate; j++)  
      /* Quasi-incidences */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>            lli= log(survp); 
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          } 
        /* Stable prevalence in each health state */  
        for(cpt=1; cpt<nlstate;cpt++){          else if  (s2==-5) { 
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>            for (j=1,survp=0. ; j<=2; j++)  
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
        }            lli= log(survp); 
     for(cpt=1; cpt<=nlstate;cpt++) {          } 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          
 interval) in state (%d): v%s%d%d.png <br>          else{
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
      for(cpt=1; cpt<=nlstate;cpt++) {          } 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          /*if(lli ==000.0)*/
      }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          ipmx +=1;
 health expectancies in states (1) and (2): e%s%d.png<br>          sw += weight[i];
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 fprintf(fichtm,"\n</body>");          /* 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]); */
 fclose(fichtm);          /* } */
 }        } /* end of wave */
       } /* end of individual */
 /******************* Gnuplot file **************/    }  else if(mle==2){
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        for(mi=1; mi<= wav[i]-1; mi++){
   int ng;          for (ii=1;ii<=nlstate+ndeath;ii++)
   strcpy(optionfilegnuplot,optionfilefiname);            for (j=1;j<=nlstate+ndeath;j++){
   strcat(optionfilegnuplot,".gp");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("Problem with file %s",optionfilegnuplot);            }
   }          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
 #ifdef windows            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fprintf(ficgp,"cd \"%s\" \n",pathc);            cov[2]=agexact;
 #endif            if(nagesqr==1)
 m=pow(2,cptcoveff);              cov[3]= agexact*agexact;
              for (kk=1; kk<=cptcovage;kk++) {
  /* 1eme*/              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   for (cpt=1; cpt<= nlstate ; cpt ++) {            }
    for (k1=1; k1<= m ; k1 ++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #ifdef windows            savm=oldm;
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            oldm=newm;
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          } /* end mult */
 #endif        
 #ifdef unix          s1=s[mw[mi][i]][i];
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          s2=s[mw[mi+1][i]][i];
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          bbh=(double)bh[mi][i]/(double)stepm; 
 #endif          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 */
           ipmx +=1;
 for (i=1; i<= nlstate ; i ++) {          sw += weight[i];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        } /* end of wave */
 }      } /* end of individual */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    }  else if(mle==3){  /* exponential inter-extrapolation */
     for (i=1; i<= nlstate ; i ++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(mi=1; mi<= wav[i]-1; mi++){
 }          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            for (j=1;j<=nlstate+ndeath;j++){
      for (i=1; i<= nlstate ; i ++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }            for(d=0; d<dh[mi][i]; d++){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            newm=savm;
 #ifdef unix            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");            cov[2]=agexact;
 #endif            if(nagesqr==1)
    }              cov[3]= agexact*agexact;
   }            for (kk=1; kk<=cptcovage;kk++) {
   /*2 eme*/              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             }
   for (k1=1; k1<= m ; k1 ++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);            savm=oldm;
                oldm=newm;
     for (i=1; i<= nlstate+1 ; i ++) {          } /* end mult */
       k=2*i;        
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          s1=s[mw[mi][i]][i];
       for (j=1; j<= nlstate+1 ; j ++) {          s2=s[mw[mi+1][i]][i];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          bbh=(double)bh[mi][i]/(double)stepm; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 }            ipmx +=1;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          sw += weight[i];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        } /* end of wave */
       for (j=1; j<= nlstate+1 ; j ++) {      } /* end of individual */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         else fprintf(ficgp," \%%*lf (\%%*lf)");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }          for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       fprintf(ficgp,"\" t\"\" w l 0,");        for(mi=1; mi<= wav[i]-1; mi++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1; j<= nlstate+1 ; j ++) {            for (j=1;j<=nlstate+ndeath;j++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }              }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          for(d=0; d<dh[mi][i]; d++){
       else fprintf(ficgp,"\" t\"\" w l 0,");            newm=savm;
     }            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            cov[2]=agexact;
              if(nagesqr==1)
   /*3eme*/              cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
   for (k1=1; k1<= m ; k1 ++) {              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
     for (cpt=1; cpt<= nlstate ; cpt ++) {            }
       k=2+nlstate*(2*cpt-2);          
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            savm=oldm;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            oldm=newm;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          } /* end mult */
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          s1=s[mw[mi][i]][i];
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
 */            lli=log(out[s1][s2] - savm[s1][s2]);
       for (i=1; i< nlstate ; i ++) {          }else{
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
       }          ipmx +=1;
     }          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   /* CV preval stat */        } /* end of wave */
     for (k1=1; k1<= m ; k1 ++) {      } /* end of individual */
     for (cpt=1; cpt<nlstate ; cpt ++) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       k=3;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
       for (i=1; i< nlstate ; i ++)            for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficgp,"+$%d",k+i+1);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                  }
       l=3+(nlstate+ndeath)*cpt;          for(d=0; d<dh[mi][i]; d++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            newm=savm;
       for (i=1; i< nlstate ; i ++) {            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
         l=3+(nlstate+ndeath)*cpt;            cov[2]=agexact;
         fprintf(ficgp,"+$%d",l+i+1);            if(nagesqr==1)
       }              cov[3]= agexact*agexact;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   }              }
            
   /* proba elementaires */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    for(i=1,jk=1; i <=nlstate; i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(k=1; k <=(nlstate+ndeath); k++){            savm=oldm;
       if (k != i) {            oldm=newm;
         for(j=1; j <=ncovmodel; j++){          } /* end mult */
                
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          s1=s[mw[mi][i]][i];
           jk++;          s2=s[mw[mi+1][i]][i];
           fprintf(ficgp,"\n");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          ipmx +=1;
       }          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/      } /* end of individual */
      for(jk=1; jk <=m; jk++) {    } /* End of if */
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        if (ng==2)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
        else    return -l;
          fprintf(ficgp,"\nset title \"Probability\"\n");  }
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);  
        i=1;  /*************** log-likelihood *************/
        for(k2=1; k2<=nlstate; k2++) {  double funcone( double *x)
          k3=i;  {
          for(k=1; k<=(nlstate+ndeath); k++) {    /* Same as likeli but slower because of a lot of printf and if */
            if (k != k2){    int i, ii, j, k, mi, d, kk;
              if(ng==2)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    double **out;
              else    double lli; /* Individual log likelihood */
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    double llt;
              ij=1;    int s1, s2;
              for(j=3; j <=ncovmodel; j++) {    double bbh, survp;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double agexact;
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /*extern weight */
                  ij++;    /* We are differentiating ll according to initial status */
                }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                else    /*for(i=1;i<imx;i++) 
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      printf(" %d\n",s[4][i]);
              }    */
              fprintf(ficgp,")/(1");    cov[1]=1.;
                
              for(k1=1; k1 <=nlstate; k1++){      for(k=1; k<=nlstate; k++) ll[k]=0.;
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
                ij=1;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                for(j=3; j <=ncovmodel; j++){      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(mi=1; mi<= wav[i]-1; mi++){
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for (ii=1;ii<=nlstate+ndeath;ii++)
                    ij++;          for (j=1;j<=nlstate+ndeath;j++){
                  }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                  else            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
                }        for(d=0; d<dh[mi][i]; d++){
                fprintf(ficgp,")");          newm=savm;
              }          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);          cov[2]=agexact;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          if(nagesqr==1)
              i=i+ncovmodel;            cov[3]= agexact*agexact;
            }          for (kk=1; kk<=cptcovage;kk++) {
          }            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
        }          }
      }  
    }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
    fclose(ficgp);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }  /* end gnuplot */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
           /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
 /*************** Moving average **************/          savm=oldm;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          oldm=newm;
         } /* end mult */
   int i, cpt, cptcod;        
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        s1=s[mw[mi][i]][i];
       for (i=1; i<=nlstate;i++)        s2=s[mw[mi+1][i]][i];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        bbh=(double)bh[mi][i]/(double)stepm; 
           mobaverage[(int)agedeb][i][cptcod]=0.;        /* bias is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){         */
       for (i=1; i<=nlstate;i++){        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          lli=log(out[s1][s2] - savm[s1][s2]);
           for (cpt=0;cpt<=4;cpt++){        } else if  (s2==-2) {
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for (j=1,survp=0. ; j<=nlstate; j++) 
           }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          lli= log(survp);
         }        }else if (mle==1){
       }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }        } else if(mle==2){
              lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 }        } 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 */
 /************** Forecasting ******************/          lli=log(out[s1][s2]); /* Original formula */
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        } else{  /* mle=0 back to 1 */
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          /*lli=log(out[s1][s2]); */ /* Original formula */
   int *popage;        } /* End of if */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        ipmx +=1;
   double *popeffectif,*popcount;        sw += weight[i];
   double ***p3mat;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char fileresf[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]); */
         if(globpr){
  agelim=AGESUP;          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;   %11.6f %11.6f %11.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
              llt +=ll[k]*gipmx/gsw;
   strcpy(fileresf,"f");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   strcat(fileresf,fileres);          }
   if((ficresf=fopen(fileresf,"w"))==NULL) {          fprintf(ficresilk," %10.6f\n", -llt);
     printf("Problem with forecast resultfile: %s\n", fileresf);        }
   }      } /* end of wave */
   printf("Computing forecasting: result on file '%s' \n", fileresf);    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   if (mobilav==1) {    if(globpr==0){ /* First time we count the contributions and weights */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      gipmx=ipmx;
     movingaverage(agedeb, fage, ageminpar, mobaverage);      gsw=sw;
   }    }
     return -l;
   stepsize=(int) (stepm+YEARM-1)/YEARM;  }
   if (stepm<=12) stepsize=1;  
    
   agelim=AGESUP;  /*************** function likelione ***********/
    void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   hstepm=1;  {
   hstepm=hstepm/stepm;    /* This routine should help understanding what is done with 
   yp1=modf(dateintmean,&yp);       the selection of individuals/waves and
   anprojmean=yp;       to check the exact contribution to the likelihood.
   yp2=modf((yp1*12),&yp);       Plotting could be done.
   mprojmean=yp;     */
   yp1=modf((yp2*30.5),&yp);    int k;
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;    if(*globpri !=0){ /* Just counts and sums, no printings */
   if(mprojmean==0) jprojmean=1;      strcpy(fileresilk,"ilk"); 
        strcat(fileresilk,fileres);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresilk);
   for(cptcov=1;cptcov<=i2;cptcov++){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      }
       k=k+1;      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresf,"\n#******");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       for(j=1;j<=cptcoveff;j++) {      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(k=1; k<=nlstate; k++) 
       }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresf,"******\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       fprintf(ficresf,"# StartingAge FinalAge");    }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
          *fretone=(*funcone)(p);
          if(*globpri !=0){
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      fclose(ficresilk);
         fprintf(ficresf,"\n");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        fflush(fichtm); 
     } 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    return;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  }
           nhstepm = nhstepm/hstepm;  
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*********** Maximum Likelihood Estimation ***************/
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
          {
           for (h=0; h<=nhstepm; h++){    int i,j, iter=0;
             if (h==(int) (calagedate+YEARM*cpt)) {    double **xi;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    double fret;
             }    double fretone; /* Only one call to likelihood */
             for(j=1; j<=nlstate+ndeath;j++) {    /*  char filerespow[FILENAMELENGTH];*/
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                #ifdef NLOPT
                 if (mobilav==1)    int creturn;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    nlopt_opt opt;
                 else {    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double *lb;
                 }    double minf; /* the minimum objective value, upon return */
                    double * p1; /* Shifted parameters from 0 instead of 1 */
               }    myfunc_data dinst, *d = &dinst;
               if (h==(int)(calagedate+12*cpt)){  #endif
                 fprintf(ficresf," %.3f", kk1);  
                          
               }    xi=matrix(1,npar,1,npar);
             }    for (i=1;i<=npar;i++)
           }      for (j=1;j<=npar;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        xi[i][j]=(i==j ? 1.0 : 0.0);
         }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       }    strcpy(filerespow,"pow"); 
     }    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
              printf("Problem with resultfile: %s\n", filerespow);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
   fclose(ficresf);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
 }    for (i=1;i<=nlstate;i++)
 /************** Forecasting ******************/      for(j=1;j<=nlstate+ndeath;j++)
 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){        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  #ifdef POWELL
   int *popage;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  #endif
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;  #ifdef NLOPT
   char filerespop[FILENAMELENGTH];  #ifdef NEWUOA
     opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  #else
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   agelim=AGESUP;  #endif
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    lb=vector(0,npar-1);
      for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    nlopt_set_lower_bounds(opt, lb);
      nlopt_set_initial_step1(opt, 0.1);
      
   strcpy(filerespop,"pop");    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   strcat(filerespop,fileres);    d->function = func;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     printf("Problem with forecast resultfile: %s\n", filerespop);    nlopt_set_min_objective(opt, myfunc, d);
   }    nlopt_set_xtol_rel(opt, ftol);
   printf("Computing forecasting: result on file '%s' \n", filerespop);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    }
     else {
   if (mobilav==1) {      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
     movingaverage(agedeb, fage, ageminpar, mobaverage);      iter=1; /* not equal */
   }    }
     nlopt_destroy(opt);
   stepsize=(int) (stepm+YEARM-1)/YEARM;  #endif
   if (stepm<=12) stepsize=1;    free_matrix(xi,1,npar,1,npar);
      fclose(ficrespow);
   agelim=AGESUP;    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
      fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   hstepm=1;    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   hstepm=hstepm/stepm;  
    }
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {  /**** Computes Hessian and covariance matrix ***/
       printf("Problem with population file : %s\n",popfile);exit(0);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     }  {
     popage=ivector(0,AGESUP);    double  **a,**y,*x,pd;
     popeffectif=vector(0,AGESUP);    double **hess;
     popcount=vector(0,AGESUP);    int i, j;
        int *indx;
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) 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);
     imx=i;    void lubksb(double **a, int npar, int *indx, double b[]) ;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    void ludcmp(double **a, int npar, int *indx, double *d) ;
   }    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    printf("\nCalculation of the hessian matrix. Wait...\n");
       k=k+1;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       fprintf(ficrespop,"\n#******");    for (i=1;i<=npar;i++){
       for(j=1;j<=cptcoveff;j++) {      printf("%d",i);fflush(stdout);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"%d",i);fflush(ficlog);
       }     
       fprintf(ficrespop,"******\n");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       fprintf(ficrespop,"# Age");      
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      /*  printf(" %f ",p[i]);
       if (popforecast==1)  fprintf(ficrespop," [Population]");          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
          }
       for (cpt=0; cpt<=0;cpt++) {    
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      for (i=1;i<=npar;i++) {
              for (j=1;j<=npar;j++)  {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        if (j>i) { 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          printf(".%d%d",i,j);fflush(stdout);
           nhstepm = nhstepm/hstepm;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                    hess[i][j]=hessij(p,delti,i,j,func,npar);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
           oldm=oldms;savm=savms;          hess[j][i]=hess[i][j];    
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            /*printf(" %lf ",hess[i][j]);*/
                }
           for (h=0; h<=nhstepm; h++){      }
             if (h==(int) (calagedate+YEARM*cpt)) {    }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    printf("\n");
             }    fprintf(ficlog,"\n");
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
               for(i=1; i<=nlstate;i++) {                  fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
                 if (mobilav==1)    
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    a=matrix(1,npar,1,npar);
                 else {    y=matrix(1,npar,1,npar);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    x=vector(1,npar);
                 }    indx=ivector(1,npar);
               }    for (i=1;i<=npar;i++)
               if (h==(int)(calagedate+12*cpt)){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    ludcmp(a,npar,indx,&pd);
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    for (j=1;j<=npar;j++) {
               }      for (i=1;i<=npar;i++) x[i]=0;
             }      x[j]=1;
             for(i=1; i<=nlstate;i++){      lubksb(a,npar,indx,x);
               kk1=0.;      for (i=1;i<=npar;i++){ 
                 for(j=1; j<=nlstate;j++){        matcov[i][j]=x[i];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      }
                 }    }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  
             }    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    for (i=1;i<=npar;i++) { 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      for (j=1;j<=npar;j++) { 
           }        printf("%.3e ",hess[i][j]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficlog,"%.3e ",hess[i][j]);
         }      }
       }      printf("\n");
        fprintf(ficlog,"\n");
   /******/    }
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    /* Recompute Inverse */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      for (i=1;i<=npar;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    ludcmp(a,npar,indx,&pd);
           nhstepm = nhstepm/hstepm;  
              /*  printf("\n#Hessian matrix recomputed#\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    for (j=1;j<=npar;j++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for (i=1;i<=npar;i++) x[i]=0;
           for (h=0; h<=nhstepm; h++){      x[j]=1;
             if (h==(int) (calagedate+YEARM*cpt)) {      lubksb(a,npar,indx,x);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for (i=1;i<=npar;i++){ 
             }        y[i][j]=x[i];
             for(j=1; j<=nlstate+ndeath;j++) {        printf("%.3e ",y[i][j]);
               kk1=0.;kk2=0;        fprintf(ficlog,"%.3e ",y[i][j]);
               for(i=1; i<=nlstate;i++) {                    }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          printf("\n");
               }      fprintf(ficlog,"\n");
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    }
             }    */
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(a,1,npar,1,npar);
         }    free_matrix(y,1,npar,1,npar);
       }    free_vector(x,1,npar);
    }    free_ivector(indx,1,npar);
   }    free_matrix(hess,1,npar,1,npar);
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   }
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);  /*************** hessian matrix ****************/
     free_vector(popeffectif,0,AGESUP);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     free_vector(popcount,0,AGESUP);  {
   }    int i;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int l=1, lmax=20;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double k1,k2;
   fclose(ficrespop);    double p2[MAXPARM+1]; /* identical to x */
 }    double res;
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 /***********************************************/    double fx;
 /**************** Main Program *****************/    int k=0,kmax=10;
 /***********************************************/    double l1;
   
 int main(int argc, char *argv[])    fx=func(x);
 {    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      l1=pow(10,l);
   double agedeb, agefin,hf;      delts=delt;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
   double fret;        p2[theta]=x[theta] +delt;
   double **xi,tmp,delta;        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         p2[theta]=x[theta]-delt;
   double dum; /* Dummy variable */        k2=func(p2)-fx;
   double ***p3mat;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   int *indx;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   char line[MAXLINE], linepar[MAXLINE];        
   char title[MAXLINE];  #ifdef DEBUGHESS
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        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);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        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);
    #endif
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   char filerest[FILENAMELENGTH];          k=kmax;
   char fileregp[FILENAMELENGTH];        }
   char popfile[FILENAMELENGTH];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          k=kmax; l=lmax*10;
   int firstobs=1, lastobs=10;        }
   int sdeb, sfin; /* Status at beginning and end */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   int c,  h , cpt,l;          delts=delt;
   int ju,jl, mi;        }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    }
   int mobilav=0,popforecast=0;    delti[theta]=delts;
   int hstepm, nhstepm;    return res; 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    
   }
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   double **prlim;  {
   double *severity;    int i;
   double ***param; /* Matrix of parameters */    int l=1, lmax=20;
   double  *p;    double k1,k2,k3,k4,res,fx;
   double **matcov; /* Matrix of covariance */    double p2[MAXPARM+1];
   double ***delti3; /* Scale */    int k;
   double *delti; /* Scale */  
   double ***eij, ***vareij;    fx=func(x);
   double **varpl; /* Variances of prevalence limits by age */    for (k=1; k<=2; k++) {
   double *epj, vepp;      for (i=1;i<=npar;i++) p2[i]=x[i];
   double kk1, kk2;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k1=func(p2)-fx;
     
   char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";      p2[thetai]=x[thetai]+delti[thetai]/k;
   char *alph[]={"a","a","b","c","d","e"}, str[4];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     
   char z[1]="c", occ;      p2[thetai]=x[thetai]-delti[thetai]/k;
 #include <sys/time.h>      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 #include <time.h>      k3=func(p2)-fx;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    
        p2[thetai]=x[thetai]-delti[thetai]/k;
   /* long total_usecs;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   struct timeval start_time, end_time;      k4=func(p2)-fx;
        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  #ifdef DEBUG
   getcwd(pathcd, size);      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);
   printf("\n%s",version);  #endif
   if(argc <=1){    }
     printf("\nEnter the parameter file name: ");    return res;
     scanf("%s",pathtot);  }
   }  
   else{  /************** Inverse of matrix **************/
     strcpy(pathtot,argv[1]);  void ludcmp(double **a, int n, int *indx, double *d) 
   }  { 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    int i,imax,j,k; 
   /*cygwin_split_path(pathtot,path,optionfile);    double big,dum,sum,temp; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    double *vv; 
   /* cutv(path,optionfile,pathtot,'\\');*/   
     vv=vector(1,n); 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    *d=1.0; 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    for (i=1;i<=n;i++) { 
   chdir(path);      big=0.0; 
   replace(pathc,path);      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
 /*-------- arguments in the command line --------*/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
   strcpy(fileres,"r");    } 
   strcat(fileres, optionfilefiname);    for (j=1;j<=n;j++) { 
   strcat(fileres,".txt");    /* Other files have txt extension */      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
   /*---------arguments file --------*/        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      } 
     printf("Problem with optionfile %s\n",optionfile);      big=0.0; 
     goto end;      for (i=j;i<=n;i++) { 
   }        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   strcpy(filereso,"o");          sum -= a[i][k]*a[k][j]; 
   strcat(filereso,fileres);        a[i][j]=sum; 
   if((ficparo=fopen(filereso,"w"))==NULL) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          big=dum; 
   }          imax=i; 
         } 
   /* Reads comments: lines beginning with '#' */      } 
   while((c=getc(ficpar))=='#' && c!= EOF){      if (j != imax) { 
     ungetc(c,ficpar);        for (k=1;k<=n;k++) { 
     fgets(line, MAXLINE, ficpar);          dum=a[imax][k]; 
     puts(line);          a[imax][k]=a[j][k]; 
     fputs(line,ficparo);          a[j][k]=dum; 
   }        } 
   ungetc(c,ficpar);        *d = -(*d); 
         vv[imax]=vv[j]; 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      } 
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);      indx[j]=imax; 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);      if (a[j][j] == 0.0) a[j][j]=TINY; 
 while((c=getc(ficpar))=='#' && c!= EOF){      if (j != n) { 
     ungetc(c,ficpar);        dum=1.0/(a[j][j]); 
     fgets(line, MAXLINE, ficpar);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     puts(line);      } 
     fputs(line,ficparo);    } 
   }    free_vector(vv,1,n);  /* Doesn't work */
   ungetc(c,ficpar);  ;
    } 
      
   covar=matrix(0,NCOVMAX,1,n);  void lubksb(double **a, int n, int *indx, double b[]) 
   cptcovn=0;  { 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    int i,ii=0,ip,j; 
     double sum; 
   ncovmodel=2+cptcovn;   
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    for (i=1;i<=n;i++) { 
        ip=indx[i]; 
   /* Read guess parameters */      sum=b[ip]; 
   /* Reads comments: lines beginning with '#' */      b[ip]=b[i]; 
   while((c=getc(ficpar))=='#' && c!= EOF){      if (ii) 
     ungetc(c,ficpar);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     fgets(line, MAXLINE, ficpar);      else if (sum) ii=i; 
     puts(line);      b[i]=sum; 
     fputs(line,ficparo);    } 
   }    for (i=n;i>=1;i--) { 
   ungetc(c,ficpar);      sum=b[i]; 
        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      b[i]=sum/a[i][i]; 
     for(i=1; i <=nlstate; i++)    } 
     for(j=1; j <=nlstate+ndeath-1; j++){  } 
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);  void pstamp(FILE *fichier)
       printf("%1d%1d",i,j);  {
       for(k=1; k<=ncovmodel;k++){    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
         fscanf(ficpar," %lf",&param[i][j][k]);  }
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);  /************ Frequencies ********************/
       }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
       fscanf(ficpar,"\n");  {  /* Some frequencies */
       printf("\n");    
       fprintf(ficparo,"\n");    int i, m, jk, j1, bool, z1,j;
     }    int first;
      double ***freq; /* Frequencies */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
   p=param[1][1];    char fileresp[FILENAMELENGTH];
      
   /* Reads comments: lines beginning with '#' */    pp=vector(1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    prop=matrix(1,nlstate,iagemin,iagemax+3);
     ungetc(c,ficpar);    strcpy(fileresp,"p");
     fgets(line, MAXLINE, ficpar);    strcat(fileresp,fileres);
     puts(line);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     fputs(line,ficparo);      printf("Problem with prevalence resultfile: %s\n", fileresp);
   }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   ungetc(c,ficpar);      exit(0);
     }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    j1=0;
   for(i=1; i <=nlstate; i++){    
     for(j=1; j <=nlstate+ndeath-1; j++){    j=cptcoveff;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);    first=1;
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
         printf(" %le",delti3[i][j][k]);    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
         fprintf(ficparo," %le",delti3[i][j][k]);    /*    j1++; */
       }    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       fscanf(ficpar,"\n");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       printf("\n");          scanf("%d", i);*/
       fprintf(ficparo,"\n");        for (i=-5; i<=nlstate+ndeath; i++)  
     }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   }            for(m=iagemin; m <= iagemax+3; m++)
   delti=delti3[1][1];              freq[i][jk][m]=0;
          
   /* Reads comments: lines beginning with '#' */        for (i=1; i<=nlstate; i++)  
   while((c=getc(ficpar))=='#' && c!= EOF){          for(m=iagemin; m <= iagemax+3; m++)
     ungetc(c,ficpar);            prop[i][m]=0;
     fgets(line, MAXLINE, ficpar);        
     puts(line);        dateintsum=0;
     fputs(line,ficparo);        k2cpt=0;
   }        for (i=1; i<=imx; i++) {
   ungetc(c,ficpar);          bool=1;
            if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
   matcov=matrix(1,npar,1,npar);            for (z1=1; z1<=cptcoveff; z1++)       
   for(i=1; i <=npar; i++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
     fscanf(ficpar,"%s",&str);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
     printf("%s",str);                bool=0;
     fprintf(ficparo,"%s",str);                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
     for(j=1; j <=i; j++){                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
       fscanf(ficpar," %le",&matcov[i][j]);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
       printf(" %.5le",matcov[i][j]);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
       fprintf(ficparo," %.5le",matcov[i][j]);              } 
     }          }
     fscanf(ficpar,"\n");   
     printf("\n");          if (bool==1){
     fprintf(ficparo,"\n");            for(m=firstpass; m<=lastpass; m++){
   }              k2=anint[m][i]+(mint[m][i]/12.);
   for(i=1; i <=npar; i++)              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     for(j=i+1;j<=npar;j++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       matcov[i][j]=matcov[j][i];                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];
   printf("\n");                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];
     /*-------- Rewriting paramater file ----------*/                }
      strcpy(rfileres,"r");    /* "Rparameterfile */                
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
      strcat(rfileres,".");    /* */                  dateintsum=dateintsum+k2;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */                  k2cpt++;
     if((ficres =fopen(rfileres,"w"))==NULL) {                }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                /*}*/
     }            }
     fprintf(ficres,"#%s\n",version);          }
            } /* end i */
     /*-------- data file ----------*/         
     if((fic=fopen(datafile,"r"))==NULL)    {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       printf("Problem with datafile: %s\n", datafile);goto end;        pstamp(ficresp);
     }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
     n= lastobs;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     severity = vector(1,maxwav);          fprintf(ficresp, "**********\n#");
     outcome=imatrix(1,maxwav+1,1,n);          fprintf(ficlog, "\n#********** Variable "); 
     num=ivector(1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     moisnais=vector(1,n);          fprintf(ficlog, "**********\n#");
     annais=vector(1,n);        }
     moisdc=vector(1,n);        for(i=1; i<=nlstate;i++) 
     andc=vector(1,n);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     agedc=vector(1,n);        fprintf(ficresp, "\n");
     cod=ivector(1,n);        
     weight=vector(1,n);        for(i=iagemin; i <= iagemax+3; i++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          if(i==iagemax+3){
     mint=matrix(1,maxwav,1,n);            fprintf(ficlog,"Total");
     anint=matrix(1,maxwav,1,n);          }else{
     s=imatrix(1,maxwav+1,1,n);            if(first==1){
     adl=imatrix(1,maxwav+1,1,n);                  first=0;
     tab=ivector(1,NCOVMAX);              printf("See log file for details...\n");
     ncodemax=ivector(1,8);            }
             fprintf(ficlog,"Age %d", i);
     i=1;          }
     while (fgets(line, MAXLINE, fic) != NULL)    {          for(jk=1; jk <=nlstate ; jk++){
       if ((i >= firstobs) && (i <=lastobs)) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                      pp[jk] += freq[jk][m][i]; 
         for (j=maxwav;j>=1;j--){          }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          for(jk=1; jk <=nlstate ; jk++){
           strcpy(line,stra);            for(m=-1, pos=0; m <=0 ; m++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              pos += freq[jk][m][i];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            if(pp[jk]>=1.e-10){
         }              if(first==1){
                        printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              if(first==1)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            }
         for (j=ncovcol;j>=1;j--){          }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }          for(jk=1; jk <=nlstate ; jk++){
         num[i]=atol(stra);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                      pp[jk] += freq[jk][m][i];
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          }       
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
         i=i+1;            posprop += prop[jk][i];
       }          }
     }          for(jk=1; jk <=nlstate ; jk++){
     /* printf("ii=%d", ij);            if(pos>=1.e-5){
        scanf("%d",i);*/              if(first==1)
   imx=i-1; /* Number of individuals */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   /* for (i=1; i<=imx; i++){            }else{
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              if(first==1)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }*/            }
    /*  for (i=1; i<=imx; i++){            if( i <= iagemax){
      if (s[4][i]==9)  s[4][i]=-1;              if(pos>=1.e-5){
      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]));}*/                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                  /*probs[i][jk][j1]= pp[jk]/pos;*/
                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   /* Calculation of the number of parameter from char model*/              }
   Tvar=ivector(1,15);              else
   Tprod=ivector(1,15);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   Tvaraff=ivector(1,15);            }
   Tvard=imatrix(1,15,1,2);          }
   Tage=ivector(1,15);                
              for(jk=-1; jk <=nlstate+ndeath; jk++)
   if (strlen(model) >1){            for(m=-1; m <=nlstate+ndeath; m++)
     j=0, j1=0, k1=1, k2=1;              if(freq[jk][m][i] !=0 ) {
     j=nbocc(model,'+');              if(first==1)
     j1=nbocc(model,'*');                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     cptcovn=j+1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     cptcovprod=j1;              }
              if(i <= iagemax)
     strcpy(modelsav,model);            fprintf(ficresp,"\n");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          if(first==1)
       printf("Error. Non available option model=%s ",model);            printf("Others in log...\n");
       goto end;          fprintf(ficlog,"\n");
     }        }
            /*}*/
     for(i=(j+1); i>=1;i--){    }
       cutv(stra,strb,modelsav,'+');    dateintmean=dateintsum/k2cpt; 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);   
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    fclose(ficresp);
       /*scanf("%d",i);*/    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       if (strchr(strb,'*')) {    free_vector(pp,1,nlstate);
         cutv(strd,strc,strb,'*');    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         if (strcmp(strc,"age")==0) {    /* End of Freq */
           cptcovprod--;  }
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);  /************ Prevalence ********************/
           cptcovage++;  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)
             Tage[cptcovage]=i;  {  
             /*printf("stre=%s ", stre);*/    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         }       in each health status at the date of interview (if between dateprev1 and dateprev2).
         else if (strcmp(strd,"age")==0) {       We still use firstpass and lastpass as another selection.
           cptcovprod--;    */
           cutv(strb,stre,strc,'V');   
           Tvar[i]=atoi(stre);    int i, m, jk, j1, bool, z1,j;
           cptcovage++;  
           Tage[cptcovage]=i;    double **prop;
         }    double posprop; 
         else {    double  y2; /* in fractional years */
           cutv(strb,stre,strc,'V');    int iagemin, iagemax;
           Tvar[i]=ncovcol+k1;    int first; /** to stop verbosity which is redirected to log file */
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;    iagemin= (int) agemin;
           Tvard[k1][1]=atoi(strc);    iagemax= (int) agemax;
           Tvard[k1][2]=atoi(stre);    /*pp=vector(1,nlstate);*/
           Tvar[cptcovn+k2]=Tvard[k1][1];    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           for (k=1; k<=lastobs;k++)    j1=0;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    
           k1++;    /*j=cptcoveff;*/
           k2=k2+2;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }    
       }    first=1;
       else {    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      /*for(i1=1; i1<=ncodemax[k1];i1++){
        /*  scanf("%d",i);*/        j1++;*/
       cutv(strd,strc,strb,'V');        
       Tvar[i]=atoi(strc);        for (i=1; i<=nlstate; i++)  
       }          for(m=iagemin; m <= iagemax+3; m++)
       strcpy(modelsav,stra);              prop[i][m]=0.0;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);       
         scanf("%d",i);*/        for (i=1; i<=imx; i++) { /* Each individual */
     }          bool=1;
 }          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   printf("cptcovprod=%d ", cptcovprod);                bool=0;
   scanf("%d ",i);*/          } 
     fclose(fic);          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     /*  if(mle==1){*/              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     if (weightopt != 1) { /* Maximisation without weights*/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for(i=1;i<=n;i++) weight[i]=1.0;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     /*-calculation of age at interview from date of interview and age at death -*/                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); 
     agev=matrix(1,maxwav,1,imx);                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]]);*/
     for (i=1; i<=imx; i++) {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       for(m=2; (m<= maxwav); m++) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                } 
          anint[m][i]=9999;              }
          s[m][i]=-1;            } /* end selection of waves */
        }          }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        }
       }        for(i=iagemin; i <= iagemax+3; i++){  
     }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
     for (i=1; i<=imx; i++)  {          } 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          
       for(m=1; (m<= maxwav); m++){          for(jk=1; jk <=nlstate ; jk++){     
         if(s[m][i] >0){            if( i <=  iagemax){ 
           if (s[m][i] >= nlstate+1) {              if(posprop>=1.e-5){ 
             if(agedc[i]>0)                probs[i][jk][j1]= prop[jk][i]/posprop;
               if(moisdc[i]!=99 && andc[i]!=9999)              } else{
                 agev[m][i]=agedc[i];                if(first==1){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                  first=0;
            else {                  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]);
               if (andc[i]!=9999){                }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              }
               agev[m][i]=-1;            } 
               }          }/* end jk */ 
             }        }/* end i */ 
           }      /*} *//* end i1 */
           else if(s[m][i] !=9){ /* Should no more exist */    } /* end j1 */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    
             if(mint[m][i]==99 || anint[m][i]==9999)    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
               agev[m][i]=1;    /*free_vector(pp,1,nlstate);*/
             else if(agev[m][i] <agemin){    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
               agemin=agev[m][i];  }  /* End of prevalence */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  
             }  /************* Waves Concatenation ***************/
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];  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)
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  {
             }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
             /*agev[m][i]=anint[m][i]-annais[i];*/       Death is a valid wave (if date is known).
             /*   agev[m][i] = age[i]+2*m;*/       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           else { /* =9 */       and mw[mi+1][i]. dh depends on stepm.
             agev[m][i]=1;       */
             s[m][i]=-1;  
           }    int i, mi, m;
         }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         else /*= 0 Unknown */       double sum=0., jmean=0.;*/
           agev[m][i]=1;    int first;
       }    int j, k=0,jk, ju, jl;
        double sum=0.;
     }    first=0;
     for (i=1; i<=imx; i++)  {    jmin=100000;
       for(m=1; (m<= maxwav); m++){    jmax=-1;
         if (s[m][i] > (nlstate+ndeath)) {    jmean=0.;
           printf("Error: Wrong value in nlstate or ndeath\n");      for(i=1; i<=imx; i++){
           goto end;      mi=0;
         }      m=firstpass;
       }      while(s[m][i] <= nlstate){
     }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           mw[++mi][i]=m;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        if(m >=lastpass)
           break;
     free_vector(severity,1,maxwav);        else
     free_imatrix(outcome,1,maxwav+1,1,n);          m++;
     free_vector(moisnais,1,n);      }/* end while */
     free_vector(annais,1,n);      if (s[m][i] > nlstate){
     /* free_matrix(mint,1,maxwav,1,n);        mi++;     /* Death is another wave */
        free_matrix(anint,1,maxwav,1,n);*/        /* if(mi==0)  never been interviewed correctly before death */
     free_vector(moisdc,1,n);           /* Only death is a correct wave */
     free_vector(andc,1,n);        mw[mi][i]=m;
       }
      
     wav=ivector(1,imx);      wav[i]=mi;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      if(mi==0){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        nbwarn++;
            if(first==0){
     /* Concatenates waves */          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          first=1;
         }
         if(first==1){
       Tcode=ivector(1,100);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        }
       ncodemax[1]=1;      } /* end mi==0 */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    } /* End individuals */
        
    codtab=imatrix(1,100,1,10);    for(i=1; i<=imx; i++){
    h=0;      for(mi=1; mi<wav[i];mi++){
    m=pow(2,cptcoveff);        if (stepm <=0)
            dh[mi][i]=1;
    for(k=1;k<=cptcoveff; k++){        else{
      for(i=1; i <=(m/pow(2,k));i++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
        for(j=1; j <= ncodemax[k]; j++){            if (agedc[i] < 2*AGESUP) {
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
            h++;              if(j==0) j=1;  /* Survives at least one month after exam */
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;              else if(j<0){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                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 */
      }                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
    }                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                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);
       codtab[1][2]=1;codtab[2][2]=2; */              }
    /* for(i=1; i <=m ;i++){              k=k+1;
       for(k=1; k <=cptcovn; k++){              if (j >= jmax){
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                jmax=j;
       }                ijmax=i;
       printf("\n");              }
       }              if (j <= jmin){
       scanf("%d",i);*/                jmin=j;
                    ijmin=i;
    /* Calculates basic frequencies. Computes observed prevalence at single age              }
        and prints on file fileres'p'. */              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                  /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          else{
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*        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]); */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
                  k=k+1;
     /* For Powell, parameters are in a vector p[] starting at p[1]            if (j >= jmax) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */              jmax=j;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              ijmax=i;
             }
     if(mle==1){            else if (j <= jmin){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              jmin=j;
     }              ijmin=i;
                }
     /*--------- results files --------------*/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);            /*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]);*/
              if(j<0){
               nberr++;
    jk=1;              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(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");              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("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            }
    for(i=1,jk=1; i <=nlstate; i++){            sum=sum+j;
      for(k=1; k <=(nlstate+ndeath); k++){          }
        if (k != i)          jk= j/stepm;
          {          jl= j -jk*stepm;
            printf("%d%d ",i,k);          ju= j -(jk+1)*stepm;
            fprintf(ficres,"%1d%1d ",i,k);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
            for(j=1; j <=ncovmodel; j++){            if(jl==0){
              printf("%f ",p[jk]);              dh[mi][i]=jk;
              fprintf(ficres,"%f ",p[jk]);              bh[mi][i]=0;
              jk++;            }else{ /* We want a negative bias in order to only have interpolation ie
            }                    * to avoid the price of an extra matrix product in likelihood */
            printf("\n");              dh[mi][i]=jk+1;
            fprintf(ficres,"\n");              bh[mi][i]=ju;
          }            }
      }          }else{
    }            if(jl <= -ju){
  if(mle==1){              dh[mi][i]=jk;
     /* Computing hessian and covariance matrix */              bh[mi][i]=jl;       /* bias is positive if real duration
     ftolhess=ftol; /* Usually correct */                                   * is higher than the multiple of stepm and negative otherwise.
     hesscov(matcov, p, npar, delti, ftolhess, func);                                   */
  }            }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            else{
     printf("# Scales (for hessian or gradient estimation)\n");              dh[mi][i]=jk+1;
      for(i=1,jk=1; i <=nlstate; i++){              bh[mi][i]=ju;
       for(j=1; j <=nlstate+ndeath; j++){            }
         if (j!=i) {            if(dh[mi][i]==0){
           fprintf(ficres,"%1d%1d",i,j);              dh[mi][i]=1; /* At least one step */
           printf("%1d%1d",i,j);              bh[mi][i]=ju; /* At least one step */
           for(k=1; k<=ncovmodel;k++){              /*  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);*/
             printf(" %.5e",delti[jk]);            }
             fprintf(ficres," %.5e",delti[jk]);          } /* end if mle */
             jk++;        }
           }      } /* end wave */
           printf("\n");    }
           fprintf(ficres,"\n");    jmean=sum/k;
         }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
       }    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
      }   }
      
     k=1;  /*********** Tricode ****************************/
     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");  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");  {
     for(i=1;i<=npar;i++){    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       /*  if (k>nlstate) k=1;    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
       i1=(i-1)/(ncovmodel*nlstate)+1;     * Boring subroutine which should only output nbcode[Tvar[j]][k]
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       printf("%s%d%d",alph[k],i1,tab[i]);*/     * nbcode[Tvar[j]][1]= 
       fprintf(ficres,"%3d",i);    */
       printf("%3d",i);  
       for(j=1; j<=i;j++){    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
         fprintf(ficres," %.5e",matcov[i][j]);    int modmaxcovj=0; /* Modality max of covariates j */
         printf(" %.5e",matcov[i][j]);    int cptcode=0; /* Modality max of covariates j */
       }    int modmincovj=0; /* Modality min of covariates j */
       fprintf(ficres,"\n");  
       printf("\n");  
       k++;    cptcoveff=0; 
     }   
        for (k=-1; k < maxncov; k++) Ndum[k]=0;
     while((c=getc(ficpar))=='#' && c!= EOF){    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);    /* Loop on covariates without age and products */
       puts(line);    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
       fputs(line,ficparo);      for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
     }                                 modality of this covariate Vj*/ 
     ungetc(c,ficpar);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
     estepm=0;                                      * If product of Vn*Vm, still boolean *:
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
     if (estepm==0 || estepm < stepm) estepm=stepm;                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
     if (fage <= 2) {        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
       bage = ageminpar;                                        modality of the nth covariate of individual i. */
       fage = agemaxpar;        if (ij > modmaxcovj)
     }          modmaxcovj=ij; 
            else if (ij < modmincovj) 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          modmincovj=ij; 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        if ((ij < -1) && (ij > NCOVMAX)){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
            exit(1);
     while((c=getc(ficpar))=='#' && c!= EOF){        }else
     ungetc(c,ficpar);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     fgets(line, MAXLINE, ficpar);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     puts(line);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     fputs(line,ficparo);        /* getting the maximum value of the modality of the covariate
   }           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   ungetc(c,ficpar);           female is 1, then modmaxcovj=1.*/
        } /* end for loop on individuals */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      cptcode=modmaxcovj;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
           /*for (i=0; i<=cptcode; i++) {*/
   while((c=getc(ficpar))=='#' && c!= EOF){      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
     ungetc(c,ficpar);        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
     fgets(line, MAXLINE, ficpar);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
     puts(line);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
     fputs(line,ficparo);        }
   }        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
   ungetc(c,ficpar);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
        } /* Ndum[-1] number of undefined modalities */
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
          If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
   fscanf(ficpar,"pop_based=%d\n",&popbased);         modmincovj=3; modmaxcovj = 7;
   fprintf(ficparo,"pop_based=%d\n",popbased);           There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
   fprintf(ficres,"pop_based=%d\n",popbased);           which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
           defining two dummy variables: variables V1_1 and V1_2.
   while((c=getc(ficpar))=='#' && c!= EOF){         nbcode[Tvar[j]][ij]=k;
     ungetc(c,ficpar);         nbcode[Tvar[j]][1]=0;
     fgets(line, MAXLINE, ficpar);         nbcode[Tvar[j]][2]=1;
     puts(line);         nbcode[Tvar[j]][3]=2;
     fputs(line,ficparo);      */
   }      ij=1; /* ij is similar to i but can jumps over null modalities */
   ungetc(c,ficpar);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          /*recode from 0 */
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            nbcode[Tvar[j]][ij]=k;  /* stores the modality k in an array nbcode. 
                                        k is a modality. If we have model=V1+V1*sex 
                                        then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
 while((c=getc(ficpar))=='#' && c!= EOF){            ij++;
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          if (ij > ncodemax[j]) break; 
     puts(line);        }  /* end of loop on */
     fputs(line,ficparo);      } /* 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*/  
   ungetc(c,ficpar);    
    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);     Ndum[ij]++; /* Might be supersed V1 + V1*age */
    } 
 /*------------ gnuplot -------------*/  
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);   ij=1;
     for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
 /*------------ free_vector  -------------*/     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
  chdir(path);     if((Ndum[i]!=0) && (i<=ncovcol)){
         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
  free_ivector(wav,1,imx);       Tvaraff[ij]=i; /*For printing (unclear) */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);       ij++;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       }else
  free_ivector(num,1,n);         Tvaraff[ij]=0;
  free_vector(agedc,1,n);   }
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   ij--;
  fclose(ficparo);   cptcoveff=ij; /*Number of total covariates*/
  fclose(ficres);  
   }
 /*--------- index.htm --------*/  
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  /*********** Health Expectancies ****************/
   
    void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   /*--------------- Prevalence limit --------------*/  
    {
   strcpy(filerespl,"pl");    /* Health expectancies, no variances */
   strcat(filerespl,fileres);    int i, j, nhstepm, hstepm, h, nstepm;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    int nhstepma, nstepma; /* Decreasing with age */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    double age, agelim, hf;
   }    double ***p3mat;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double eip;
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");    pstamp(ficreseij);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   fprintf(ficrespl,"\n");    fprintf(ficreseij,"# Age");
      for(i=1; i<=nlstate;i++){
   prlim=matrix(1,nlstate,1,nlstate);      for(j=1; j<=nlstate;j++){
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficreseij," e%1d%1d ",i,j);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficreseij," e%1d. ",i);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficreseij,"\n");
   k=0;  
   agebase=ageminpar;    
   agelim=agemaxpar;    if(estepm < stepm){
   ftolpl=1.e-10;      printf ("Problem %d lower than %d\n",estepm, stepm);
   i1=cptcoveff;    }
   if (cptcovn < 1){i1=1;}    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   for(cptcov=1;cptcov<=i1;cptcov++){     * This is mainly to measure the difference between two models: for example
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     * if stepm=24 months pijx are given only every 2 years and by summing them
         k=k+1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/     * progression in between and thus overestimating or underestimating according
         fprintf(ficrespl,"\n#******");     * to the curvature of the survival function. If, for the same date, we 
         for(j=1;j<=cptcoveff;j++)     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * to compare the new estimate of Life expectancy with the same linear 
         fprintf(ficrespl,"******\n");     * hypothesis. A more precise result, taking into account a more precise
             * curvature will be obtained if estepm is as small as stepm. */
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* For example we decided to compute the life expectancy with the smallest unit */
           fprintf(ficrespl,"%.0f",age );    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           for(i=1; i<=nlstate;i++)       nhstepm is the number of hstepm from age to agelim 
           fprintf(ficrespl," %.5f", prlim[i][i]);       nstepm is the number of stepm from age to agelin. 
           fprintf(ficrespl,"\n");       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
   fclose(ficrespl);       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 
   /*------------- h Pij x at various ages ------------*/       results. So we changed our mind and took the option of the best precision.
      */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    agelim=AGESUP;
   }    /* If stepm=6 months */
   printf("Computing pij: result on file '%s' \n", filerespij);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   stepsize=(int) (stepm+YEARM-1)/YEARM;      
   /*if (stepm<=24) stepsize=2;*/  /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   agelim=AGESUP;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   hstepm=stepsize*YEARM; /* Every year of age */    /* if (stepm >= YEARM) hstepm=1;*/
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    for (age=bage; age<=fage; age ++){ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       k=k+1;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         fprintf(ficrespij,"\n#****** ");      /* if (stepm >= YEARM) hstepm=1;*/
         for(j=1;j<=cptcoveff;j++)      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");      /* If stepm=6 months */
              /* Computed by stepm unit matrices, product of hstepma matrices, stored
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
           oldm=oldms;savm=savms;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        
           fprintf(ficrespij,"# Age");      printf("%d|",(int)age);fflush(stdout);
           for(i=1; i<=nlstate;i++)      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
             for(j=1; j<=nlstate+ndeath;j++)      
               fprintf(ficrespij," %1d-%1d",i,j);      /* Computing expectancies */
           fprintf(ficrespij,"\n");      for(i=1; i<=nlstate;i++)
            for (h=0; h<=nhstepm; h++){        for(j=1; j<=nlstate;j++)
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             for(i=1; i<=nlstate;i++)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               for(j=1; j<=nlstate+ndeath;j++)            
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            /* 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(ficrespij,"\n");  
              }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");      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];
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
   fclose(ficrespij);        fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
   /*---------- Forecasting ------------------*/      
   if((stepm == 1) && (strcmp(model,".")==0)){    }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    printf("\n");
   }    fprintf(ficlog,"\n");
   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);  
   }  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[] )
    
   {
   /*---------- Health expectancies and variances ------------*/    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
   strcpy(filerest,"t");    */
   strcat(filerest,fileres);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   if((ficrest=fopen(filerest,"w"))==NULL) {    int nhstepma, nstepma; /* Decreasing with age */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    double age, agelim, hf;
   }    double ***p3matp, ***p3matm, ***varhe;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
   strcpy(filerese,"e");    double ***gradg, ***trgradg;
   strcat(filerese,fileres);    int theta;
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double eip, vip;
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
  strcpy(fileresv,"v");    xm=vector(1,npar);
   strcat(fileresv,fileres);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    
   }    pstamp(ficresstdeij);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   calagedate=-1;    fprintf(ficresstdeij,"# Age");
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
   k=0;        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficresstdeij," e%1d. ",i);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;    fprintf(ficresstdeij,"\n");
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    pstamp(ficrescveij);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       fprintf(ficrest,"******\n");    fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       fprintf(ficreseij,"\n#****** ");      for(j=1; j<=nlstate;j++){
       for(j=1;j<=cptcoveff;j++)        cptj= (j-1)*nlstate+i;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(i2=1; i2<=nlstate;i2++)
       fprintf(ficreseij,"******\n");          for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
       fprintf(ficresvij,"\n#****** ");            if(cptj2 <= cptj)
       for(j=1;j<=cptcoveff;j++)              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
       fprintf(ficresvij,"******\n");      }
     fprintf(ficrescveij,"\n");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    
       oldm=oldms;savm=savms;    if(estepm < stepm){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        printf ("Problem %d lower than %d\n",estepm, stepm);
      }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    else  hstepm=estepm;   
       oldm=oldms;savm=savms;    /* We compute the life expectancy from trapezoids spaced every estepm months
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);     * 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
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");     * to the curvature of the survival function. If, for the same date, we 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       fprintf(ficrest,"\n");     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
       epj=vector(1,nlstate+1);     * curvature will be obtained if estepm is as small as stepm. */
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* For example we decided to compute the life expectancy with the smallest unit */
         if (popbased==1) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           for(i=1; i<=nlstate;i++)       nhstepm is the number of hstepm from age to agelim 
             prlim[i][i]=probs[(int)age][i][k];       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 */
         fprintf(ficrest," %4.0f",age);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       survival function given by stepm (the optimization length). Unfortunately it
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       means that if the survival funtion is printed only each two years of age and if
             epj[j] += prlim[i][i]*eij[i][j][(int)age];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/       results. So we changed our mind and took the option of the best precision.
           }    */
           epj[nlstate+1] +=epj[j];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         }  
     /* If stepm=6 months */
         for(i=1, vepp=0.;i <=nlstate;i++)    /* nhstepm age range expressed in number of stepm */
           for(j=1;j <=nlstate;j++)    agelim=AGESUP;
             vepp += vareij[i][j][(int)age];    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         for(j=1;j <=nlstate;j++){    /* if (stepm >= YEARM) hstepm=1;*/
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         }    
         fprintf(ficrest,"\n");    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);
 free_matrix(mint,1,maxwav,1,n);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     free_vector(weight,1,n);  
   fclose(ficreseij);    for (age=bage; age<=fage; age ++){ 
   fclose(ficresvij);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   fclose(ficrest);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fclose(ficpar);      /* if (stepm >= YEARM) hstepm=1;*/
   free_vector(epj,1,nlstate+1);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    
   /*------- Variance limit prevalence------*/        /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
   strcpy(fileresvpl,"vpl");         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   strcat(fileresvpl,fileres);      
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);      /* Computing  Variances of health expectancies */
   }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);         decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
   k=0;        for(i=1; i<=npar; i++){ 
   for(cptcov=1;cptcov<=i1;cptcov++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       k=k+1;        }
       fprintf(ficresvpl,"\n#****** ");        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       for(j=1;j<=cptcoveff;j++)        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficresvpl,"******\n");        for(j=1; j<= nlstate; j++){
                for(i=1; i<=nlstate; i++){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            for(h=0; h<=nhstepm-1; h++){
       oldm=oldms;savm=savms;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     }            }
  }          }
         }
   fclose(ficresvpl);       
         for(ij=1; ij<= nlstate*nlstate; ij++)
   /*---------- End : free ----------------*/          for(h=0; h<=nhstepm-1; h++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
            }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      }/* End theta */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      
        
        for(h=0; h<=nhstepm-1; h++)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        for(j=1; j<=nlstate*nlstate;j++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          for(theta=1; theta <=npar; theta++)
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            trgradg[h][j][theta]=gradg[h][theta][j];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      
    
   free_matrix(matcov,1,npar,1,npar);       for(ij=1;ij<=nlstate*nlstate;ij++)
   free_vector(delti,1,npar);        for(ji=1;ji<=nlstate*nlstate;ji++)
   free_matrix(agev,1,maxwav,1,imx);          varhe[ij][ji][(int)age] =0.;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
        printf("%d|",(int)age);fflush(stdout);
   if(erreur >0)       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     printf("End of Imach with error or warning %d\n",erreur);       for(h=0;h<=nhstepm-1;h++){
   else   printf("End of Imach\n");        for(k=0;k<=nhstepm-1;k++){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          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]);
   /* 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(ij=1;ij<=nlstate*nlstate;ij++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/            for(ji=1;ji<=nlstate*nlstate;ji++)
   /*------ End -----------*/              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
  end:  
 #ifdef windows      /* Computing expectancies */
   /* chdir(pathcd);*/      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 #endif      for(i=1; i<=nlstate;i++)
  /*system("wgnuplot graph.plt");*/        for(j=1; j<=nlstate;j++)
  /*system("../gp37mgw/wgnuplot graph.plt");*/          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
  /*system("cd ../gp37mgw");*/            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            
  strcpy(plotcmd,GNUPLOTPROGRAM);            /* 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]);*/
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);          }
  system(plotcmd);  
       fprintf(ficresstdeij,"%3.0f",age );
 #ifdef windows      for(i=1; i<=nlstate;i++){
   while (z[0] != 'q') {        eip=0.;
     /* chdir(path); */        vip=0.;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        for(j=1; j<=nlstate;j++){
     scanf("%s",z);          eip += eij[i][j][(int)age];
     if (z[0] == 'c') system("./imach");          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     else if (z[0] == 'e') system(optionfilehtm);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     else if (z[0] == 'g') system(plotcmd);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     else if (z[0] == 'q') exit(0);        }
   }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
 #endif      }
 }      fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           if(nagesqr==1)
             cov[3]= age*age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
     for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficgp,"# initial state %d\n",i);
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           fprintf(ficgp,"#   current state %d\n",k);
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
             jk++; 
           }
           fprintf(ficgp,"\n");
         }
       }
      }
     fprintf(ficgp,"##############\n#\n");
   
     /*goto avoid;*/
     fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
     fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
     fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
     fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
     fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
     fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
     fprintf(ficgp,"#\n");
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        fprintf(ficgp,"# ng=%d\n",ng);
        fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"#    jk=%d\n",jk);
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  if(nagesqr==0)
                    fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                else
                  if(nagesqr==0)
                    fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel-nagesqr; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){ 
                  if(nagesqr==0)
                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
     
                  ij=1;
                  for(j=3; j <=ncovmodel-nagesqr; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
      * - nagesqr = 1 if age*age in the model, otherwise 0.
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
      * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
     char *strpt;
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       strcpy(modelsav,model); 
       if ((strpt=strstr(model,"age*age")) !=0){
         printf(" strpt=%s, model=%s\n",strpt, model);
         if(strpt != model){
         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
    corresponding column of parameters.\n",model);
         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
    corresponding column of parameters.\n",model); fflush(ficlog);
         return 1;
       }
   
         nagesqr=1;
         if (strstr(model,"+age*age") !=0)
           substrchaine(modelsav, model, "+age*age");
         else if (strstr(model,"age*age+") !=0)
           substrchaine(modelsav, model, "age*age+");
         else 
           substrchaine(modelsav, model, "age*age");
       }else
         nagesqr=0;
       if (strlen(modelsav) >1){
         j=nbocc(modelsav,'+'); /**< j=Number of '+' */
         j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
         cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
         cptcovt= j+1; /* Number of total covariates in the model, not including
                      * cst, age and age*age 
                      * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated 
                     * separately: ncovn=4- 2=2 (V1+V3). */
         cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
         cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
   
       
         /*   Design
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
          *  <          ncovcol=8                >
          * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
          *   k=  1    2      3       4     5       6      7        8
          *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
          *  covar[k,i], value of kth covariate if not including age for individual i:
          *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
          *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
          *  Tage[++cptcovage]=k
          *       if products, new covar are created after ncovcol with k1
          *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
          *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
          *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
          *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
          *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
          *  <          ncovcol=8                >
          *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
          *          k=  1    2      3       4     5       6      7        8    9   10   11  12
          *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
          * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          * p Tprod[1]@2={                         6, 5}
          *p Tvard[1][1]@4= {7, 8, 5, 6}
          * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
          *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          *How to reorganize?
          * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
          * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          *       {2,   1,     4,      8,    5,      6,     3,       7}
          * Struct []
          */
   
         /* This loop fills the array Tvar from the string 'model'.*/
         /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
         /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
         /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
         /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
         /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
         /*        k=1 Tvar[1]=2 (from V2) */
         /*        k=5 Tvar[5] */
         /* for (k=1; k<=cptcovn;k++) { */
         /*        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
         /*        } */
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
         /*
          * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
         for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
         cptcovage=0;
         for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                            modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
           if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
           /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
           /*scanf("%d",i);*/
           if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
             cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
             if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
               /* covar is not filled and then is empty */
               cptcovprod--;
               cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
               Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
               cptcovage++; /* Sums the number of covariates which include age as a product */
               Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
               /*printf("stre=%s ", stre);*/
             } else if (strcmp(strd,"age")==0) { /* or age*Vn */
               cptcovprod--;
               cutl(stre,strb,strc,'V');
               Tvar[k]=atoi(stre);
               cptcovage++;
               Tage[cptcovage]=k;
             } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
               /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
               cptcovn++;
               cptcovprodnoage++;k1++;
               cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
               Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                      because this model-covariate is a construction we invent a new column
                                      ncovcol + k1
                                      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                      Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
               cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
               Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
               Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
               Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
               k2=k2+2;
               Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
               Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
               for (i=1; i<=lastobs;i++){
                 /* Computes the new covariate which is a product of
                    covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                 covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
               }
             } /* End age is not in the model */
           } /* End if model includes a product */
           else { /* no more sum */
             /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
             /*  scanf("%d",i);*/
             cutl(strd,strc,strb,'V');
             ks++; /**< Number of simple covariates */
             cptcovn++;
             Tvar[k]=atoi(strd);
           }
           strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
           /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
             scanf("%d",i);*/
         } /* end of loop + on total covariates */
       } /* end if strlen(modelsave == 0) age*age might exist */
     } /* end if strlen(model == 0) */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           return 0;
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
           return 0;
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Main Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /* Main ---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
       model[strlen(model)-1]='\0';
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     if(model[0]=='#'|| model[0]== '\0'){
       printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
    'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
    'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
       if(mle != -1){
         printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
         exit(1);
       }
     }
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
     else
       ncovmodel=2; /* Constant and age */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) { /* Main Wizard */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*  Main data
      */
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
   /* Main decodemodel */
   
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] is the maximum value of this jth covariate */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              * For k=4 covariates, h goes from 1 to 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
              *     h\k   1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /* codtab[12][3]=1; */
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /* Initialisation of ----------- gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
   
   
     /* Initialisation of --------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
       /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
       /*     gsl_vector_set(x, 0, 0.0268); */
       /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 mortality only */
     /* Standard maximisation */
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* again, to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%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);
   
       /* Other stuffs, more or less useful */    
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /* Other results (useful)*/
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
    
       /* ------ Other prevalence ratios------------ */
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
   #ifdef WIN32
      if (_chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n",path);
      if(_getcwd(pathcd,MAXLINE) > 0)
   #else
      if(chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n", path);
      if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.46  
changed lines
  Added in v.1.187


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