Diff for /imach/src/imach.c between versions 1.7 and 1.189

version 1.7, 2001/05/02 17:50:24 version 1.189, 2015/04/30 14:45:16
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.189  2015/04/30 14:45:16  brouard
   individuals from different ages are interviewed on their health status    Summary: 0.98q2
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.188  2015/04/30 08:27:53  brouard
   Health expectancies are computed from the transistions observed between    *** empty log message ***
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.187  2015/04/29 09:11:15  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    *** empty log message ***
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.186  2015/04/23 12:01:52  brouard
   to be observed in state i at the first wave. Therefore the model is:    Summary: V1*age is working now, version 0.98q1
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    Some codes had been disabled in order to simplify and Vn*age was
   age", you should modify the program where the markup    working in the optimization phase, ie, giving correct MLE parameters,
     *Covariates have to be included here again* invites you to do it.    but, as usual, outputs were not correct and program core dumped.
   More covariates you add, less is the speed of the convergence.  
     Revision 1.185  2015/03/11 13:26:42  brouard
   The advantage that this computer programme claims, comes from that if the    Summary: Inclusion of compile and links command line for Intel Compiler
   delay between waves is not identical for each individual, or if some  
   individual missed an interview, the information is not rounded or lost, but    Revision 1.184  2015/03/11 11:52:39  brouard
   taken into account using an interpolation or extrapolation.    Summary: Back from Windows 8. Intel Compiler
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    Revision 1.183  2015/03/10 20:34:32  brouard
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Summary: 0.98q0, trying with directest, mnbrak fixed
   unobserved intermediate  states. This elementary transition (by month or  
   quarter trimester, semester or year) is model as a multinomial logistic.    We use directest instead of original Powell test; probably no
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    incidence on the results, but better justifications;
   and the contribution of each individual to the likelihood is simply hPijx.    We fixed Numerical Recipes mnbrak routine which was wrong and gave
     wrong results.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.182  2015/02/12 08:19:57  brouard
      Summary: Trying to keep directest which seems simpler and more general
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Author: Nicolas Brouard
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.181  2015/02/11 23:22:24  brouard
   from the European Union.    Summary: Comments on Powell added
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Author:
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.180  2015/02/11 17:33:45  brouard
      Summary: Finishing move from main to function (hpijx and prevalence_limit)
 #include <math.h>  
 #include <stdio.h>    Revision 1.179  2015/01/04 09:57:06  brouard
 #include <stdlib.h>    Summary: back to OS/X
 #include <unistd.h>  
     Revision 1.178  2015/01/04 09:35:48  brouard
 #define MAXLINE 256    *** empty log message ***
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.177  2015/01/03 18:40:56  brouard
 #define windows    Summary: Still testing ilc32 on OSX
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.176  2015/01/03 16:45:04  brouard
     *** empty log message ***
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.174  2015/01/03 16:15:49  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Summary: Still in cross-compilation
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.173  2015/01/03 12:06:26  brouard
 #define YEARM 12. /* Number of months per year */    Summary: trying to detect cross-compilation
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.172  2014/12/27 12:07:47  brouard
     Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   
 int nvar;    Revision 1.171  2014/12/23 13:26:59  brouard
 static int cptcov;    Summary: Back from Visual C
 int cptcovn, cptcovage=0, cptcoveff=0;  
 int npar=NPARMAX;    Still problem with utsname.h on Windows
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.170  2014/12/23 11:17:12  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Summary: Cleaning some \%% back to %%
   
 int *wav; /* Number of waves for this individuual 0 is possible */    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 int maxwav; /* Maxim number of waves */  
 int mle, weightopt;    Revision 1.169  2014/12/22 23:08:31  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Summary: 0.98p
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    Revision 1.168  2014/12/22 15:17:42  brouard
 FILE *ficgp, *fichtm;    Summary: update
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.167  2014/12/22 13:50:56  brouard
  FILE  *ficresvij;    Summary: Testing uname and compiler version and if compiled 32 or 64
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Testing on Linux 64
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.166  2014/12/22 11:40:47  brouard
 #define NR_END 1    *** empty log message ***
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
 #define NRANSI  
 #define ITMAX 200    * imach.c (Module): Merging 1.61 to 1.162
   
 #define TOL 2.0e-4    Revision 1.164  2014/12/16 10:52:11  brouard
     Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    * imach.c (Module): Merging 1.61 to 1.162
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.163  2014/12/16 10:30:11  brouard
 #define GOLD 1.618034    * imach.c (Module): Merging 1.61 to 1.162
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.162  2014/09/25 11:43:39  brouard
     Summary: temporary backup 0.99!
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.1  2014/09/16 11:06:58  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Summary: With some code (wrong) for nlopt
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Author:
 #define rint(a) floor(a+0.5)  
     Revision 1.161  2014/09/15 20:41:41  brouard
 static double sqrarg;    Summary: Problem with macro SQR on Intel compiler
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.160  2014/09/02 09:24:05  brouard
     *** empty log message ***
 int imx;  
 int stepm;    Revision 1.159  2014/09/01 10:34:10  brouard
 /* Stepm, step in month: minimum step interpolation*/    Summary: WIN32
     Author: Brouard
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.158  2014/08/27 17:11:51  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    *** empty log message ***
 double **pmmij;  
     Revision 1.157  2014/08/27 16:26:55  brouard
 double *weight;    Summary: Preparing windows Visual studio version
 int **s; /* Status */    Author: Brouard
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    In order to compile on Visual studio, time.h is now correct and time_t
     and tm struct should be used. difftime should be used but sometimes I
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    just make the differences in raw time format (time(&now).
 double ftolhess; /* Tolerance for computing hessian */    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name )    Revision 1.156  2014/08/25 20:10:10  brouard
 {    *** empty log message ***
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
    l1 = strlen( path );                 /* length of path */    Author: Brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.154  2014/06/20 17:32:08  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    Summary: Outputs now all graphs of convergence to period prevalence
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
       if ( getwd( dirc ) == NULL ) {    Author: Brouard
 #else  
       extern char       *getcwd( );    Revision 1.152  2014/06/18 17:54:09  brouard
     Summary: open browser, use gnuplot on same dir than imach if not found in the path
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.151  2014/06/18 16:43:30  brouard
          return( GLOCK_ERROR_GETCWD );    *** empty log message ***
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.150  2014/06/18 16:42:35  brouard
    } else {                             /* strip direcotry from path */    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
       s++;                              /* after this, the filename */    Author: brouard
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.149  2014/06/18 15:51:14  brouard
       strcpy( name, s );                /* save file name */    Summary: Some fixes in parameter files errors
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Author: Nicolas Brouard
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.148  2014/06/17 17:38:48  brouard
    l1 = strlen( dirc );                 /* length of directory */    Summary: Nothing new
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Author: Brouard
    return( 0 );                         /* we're done */  
 }    Just a new packaging for OS/X version 0.98nS
   
     Revision 1.147  2014/06/16 10:33:11  brouard
 /******************************************/    *** empty log message ***
   
 void replace(char *s, char*t)    Revision 1.146  2014/06/16 10:20:28  brouard
 {    Summary: Merge
   int i;    Author: Brouard
   int lg=20;  
   i=0;    Merge, before building revised version.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.145  2014/06/10 21:23:15  brouard
     (s[i] = t[i]);    Summary: Debugging with valgrind
     if (t[i]== '\\') s[i]='/';    Author: Nicolas Brouard
   }  
 }    Lot of changes in order to output the results with some covariates
     After the Edimburgh REVES conference 2014, it seems mandatory to
 int nbocc(char *s, char occ)    improve the code.
 {    No more memory valgrind error but a lot has to be done in order to
   int i,j=0;    continue the work of splitting the code into subroutines.
   int lg=20;    Also, decodemodel has been improved. Tricode is still not
   i=0;    optimal. nbcode should be improved. Documentation has been added in
   lg=strlen(s);    the source code.
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.143  2014/01/26 09:45:38  brouard
   }    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   return j;  
 }    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.142  2014/01/26 03:57:36  brouard
   int i,lg,j,p=0;    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.141  2014/01/26 02:42:01  brouard
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.140  2011/09/02 10:37:54  brouard
     (u[j] = t[j]);    Summary: times.h is ok with mingw32 now.
   }  
      u[p]='\0';    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.
    for(j=0; j<= lg; j++) {    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.138  2010/04/30 18:19:40  brouard
 }    *** empty log message ***
   
 /********************** nrerror ********************/    Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
 void nrerror(char error_text[])    than V1+V2. A lot of change to be done. Unstable.
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.136  2010/04/26 20:30:53  brouard
   fprintf(stderr,"%s\n",error_text);    (Module): merging some libgsl code. Fixing computation
   exit(1);    of likelione (using inter/intrapolation if mle = 0) in order to
 }    get same likelihood as if mle=1.
 /*********************** vector *******************/    Some cleaning of code and comments added.
 double *vector(int nl, int nh)  
 {    Revision 1.135  2009/10/29 15:33:14  brouard
   double *v;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.134  2009/10/29 13:18:53  brouard
   return v-nl+NR_END;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 }  
     Revision 1.133  2009/07/06 10:21:25  brouard
 /************************ free vector ******************/    just nforces
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.132  2009/07/06 08:22:05  brouard
   free((FREE_ARG)(v+nl-NR_END));    Many tings
 }  
     Revision 1.131  2009/06/20 16:22:47  brouard
 /************************ivector *******************************/    Some dimensions resccaled
 int *ivector(long nl,long nh)  
 {    Revision 1.130  2009/05/26 06:44:34  brouard
   int *v;    (Module): Max Covariate is now set to 20 instead of 8. A
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    lot of cleaning with variables initialized to 0. Trying to make
   if (!v) nrerror("allocation failure in ivector");    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   return v-nl+NR_END;  
 }    Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.128  2006/06/30 13:02:05  brouard
 {    (Module): Clarifications on computing e.j
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 /******************* imatrix *******************************/    imach-114 because nhstepm was no more computed in the age
 int **imatrix(long nrl, long nrh, long ncl, long nch)    loop. Now we define nhstepma in the age loop.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Module): In order to speed up (in case of numerous covariates) we
 {    compute health expectancies (without variances) in a first step
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    and then all the health expectancies with variances or standard
   int **m;    deviation (needs data from the Hessian matrices) which slows the
      computation.
   /* allocate pointers to rows */    In the future we should be able to stop the program is only health
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    expectancies and graph are needed without standard deviations.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.126  2006/04/28 17:23:28  brouard
   m -= nrl;    (Module): Yes the sum of survivors was wrong since
      imach-114 because nhstepm was no more computed in the age
      loop. Now we define nhstepma in the age loop.
   /* allocate rows and set pointers to them */    Version 0.98h
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.125  2006/04/04 15:20:31  lievre
   m[nrl] += NR_END;    Errors in calculation of health expectancies. Age was not initialized.
   m[nrl] -= ncl;    Forecasting file added.
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.124  2006/03/22 17:13:53  lievre
      Parameters are printed with %lf instead of %f (more numbers after the comma).
   /* return pointer to array of pointers to rows */    The log-likelihood is printed in the log file
   return m;  
 }    Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
 /****************** free_imatrix *************************/    name. <head> headers where missing.
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    * imach.c (Module): Weights can have a decimal point as for
       long nch,ncl,nrh,nrl;    English (a comma might work with a correct LC_NUMERIC environment,
      /* free an int matrix allocated by imatrix() */    otherwise the weight is truncated).
 {    Modification of warning when the covariates values are not 0 or
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    1.
   free((FREE_ARG) (m+nrl-NR_END));    Version 0.98g
 }  
     Revision 1.122  2006/03/20 09:45:41  brouard
 /******************* matrix *******************************/    (Module): Weights can have a decimal point as for
 double **matrix(long nrl, long nrh, long ncl, long nch)    English (a comma might work with a correct LC_NUMERIC environment,
 {    otherwise the weight is truncated).
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Modification of warning when the covariates values are not 0 or
   double **m;    1.
     Version 0.98g
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.121  2006/03/16 17:45:01  lievre
   m += NR_END;    * imach.c (Module): Comments concerning covariates added
   m -= nrl;  
     * imach.c (Module): refinements in the computation of lli if
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    status=-2 in order to have more reliable computation if stepm is
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    not 1 month. Version 0.98f
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    status=-2 in order to have more reliable computation if stepm is
   return m;    not 1 month. Version 0.98f
 }  
     Revision 1.119  2006/03/15 17:42:26  brouard
 /*************************free matrix ************************/    (Module): Bug if status = -2, the loglikelihood was
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    computed as likelihood omitting the logarithm. Version O.98e
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.118  2006/03/14 18:20:07  brouard
   free((FREE_ARG)(m+nrl-NR_END));    (Module): varevsij Comments added explaining the second
 }    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /******************* ma3x *******************************/    (Module): Function pstamp added
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    (Module): Version 0.98d
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.117  2006/03/14 17:16:22  brouard
   double ***m;    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Function pstamp added
   m += NR_END;    (Module): Version 0.98d
   m -= nrl;  
     Revision 1.116  2006/03/06 10:29:27  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Variance-covariance wrong links and
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    varian-covariance of ej. is needed (Saito).
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Revision 1.114  2006/02/26 12:57:58  brouard
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    (Module): Some improvements in processing parameter
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    filename with strsep.
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Revision 1.113  2006/02/24 14:20:24  brouard
   for (j=ncl+1; j<=nch; j++)    (Module): Memory leaks checks with valgrind and:
     m[nrl][j]=m[nrl][j-1]+nlay;    datafile was not closed, some imatrix were not freed and on matrix
      allocation too.
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Revision 1.112  2006/01/30 09:55:26  brouard
     for (j=ncl+1; j<=nch; j++)    (Module): Back to gnuplot.exe instead of wgnuplot.exe
       m[i][j]=m[i][j-1]+nlay;  
   }    Revision 1.111  2006/01/25 20:38:18  brouard
   return m;    (Module): Lots of cleaning and bugs added (Gompertz)
 }    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Revision 1.110  2006/01/25 00:51:50  brouard
 {    (Module): Lots of cleaning and bugs added (Gompertz)
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.109  2006/01/24 19:37:15  brouard
   free((FREE_ARG)(m+nrl-NR_END));    (Module): Comments (lines starting with a #) are allowed in data.
 }  
     Revision 1.108  2006/01/19 18:05:42  lievre
 /***************** f1dim *************************/    Gnuplot problem appeared...
 extern int ncom;    To be fixed
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    Revision 1.107  2006/01/19 16:20:37  brouard
      Test existence of gnuplot in imach path
 double f1dim(double x)  
 {    Revision 1.106  2006/01/19 13:24:36  brouard
   int j;    Some cleaning and links added in html output
   double f;  
   double *xt;    Revision 1.105  2006/01/05 20:23:19  lievre
      *** empty log message ***
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Revision 1.104  2005/09/30 16:11:43  lievre
   f=(*nrfunc)(xt);    (Module): sump fixed, loop imx fixed, and simplifications.
   free_vector(xt,1,ncom);    (Module): If the status is missing at the last wave but we know
   return f;    that the person is alive, then we can code his/her status as -2
 }    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 /*****************brent *************************/    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    the healthy state at last known wave). Version is 0.98
 {  
   int iter;    Revision 1.103  2005/09/30 15:54:49  lievre
   double a,b,d,etemp;    (Module): sump fixed, loop imx fixed, and simplifications.
   double fu,fv,fw,fx;  
   double ftemp;    Revision 1.102  2004/09/15 17:31:30  brouard
   double p,q,r,tol1,tol2,u,v,w,x,xm;    Add the possibility to read data file including tab characters.
   double e=0.0;  
      Revision 1.101  2004/09/15 10:38:38  brouard
   a=(ax < cx ? ax : cx);    Fix on curr_time
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.100  2004/07/12 18:29:06  brouard
   fw=fv=fx=(*f)(x);    Add version for Mac OS X. Just define UNIX in Makefile
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    Revision 1.99  2004/06/05 08:57:40  brouard
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    *** empty log message ***
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    Revision 1.98  2004/05/16 15:05:56  brouard
 #ifdef DEBUG    New version 0.97 . First attempt to estimate force of mortality
     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);    directly from the data i.e. without the need of knowing the health
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    state at each age, but using a Gompertz model: log u =a + b*age .
 #endif    This is the basic analysis of mortality and should be done before any
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    other analysis, in order to test if the mortality estimated from the
       *xmin=x;    cross-longitudinal survey is different from the mortality estimated
       return fx;    from other sources like vital statistic data.
     }  
     ftemp=fu;    The same imach parameter file can be used but the option for mle should be -3.
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    Agnès, who wrote this part of the code, tried to keep most of the
       q=(x-v)*(fx-fw);    former routines in order to include the new code within the former code.
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);    The output is very simple: only an estimate of the intercept and of
       if (q > 0.0) p = -p;    the slope with 95% confident intervals.
       q=fabs(q);  
       etemp=e;    Current limitations:
       e=d;    A) Even if you enter covariates, i.e. with the
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    B) There is no computation of Life Expectancy nor Life Table.
       else {  
         d=p/q;    Revision 1.97  2004/02/20 13:25:42  lievre
         u=x+d;    Version 0.96d. Population forecasting command line is (temporarily)
         if (u-a < tol2 || b-u < tol2)    suppressed.
           d=SIGN(tol1,xm-x);  
       }    Revision 1.96  2003/07/15 15:38:55  brouard
     } else {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    rewritten within the same printf. Workaround: many printfs.
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    Revision 1.95  2003/07/08 07:54:34  brouard
     fu=(*f)(u);    * imach.c (Repository):
     if (fu <= fx) {    (Repository): Using imachwizard code to output a more meaningful covariance
       if (u >= x) a=x; else b=x;    matrix (cov(a12,c31) instead of numbers.
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)    Revision 1.94  2003/06/27 13:00:02  brouard
         } else {    Just cleaning
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {    Revision 1.93  2003/06/25 16:33:55  brouard
             v=w;    (Module): On windows (cygwin) function asctime_r doesn't
             w=u;    exist so I changed back to asctime which exists.
             fv=fw;    (Module): Version 0.96b
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {    Revision 1.92  2003/06/25 16:30:45  brouard
             v=u;    (Module): On windows (cygwin) function asctime_r doesn't
             fv=fu;    exist so I changed back to asctime which exists.
           }  
         }    Revision 1.91  2003/06/25 15:30:29  brouard
   }    * imach.c (Repository): Duplicated warning errors corrected.
   nrerror("Too many iterations in brent");    (Repository): Elapsed time after each iteration is now output. It
   *xmin=x;    helps to forecast when convergence will be reached. Elapsed time
   return fx;    is stamped in powell.  We created a new html file for the graphs
 }    concerning matrix of covariance. It has extension -cov.htm.
   
 /****************** mnbrak ***********************/    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    mle=-1 a template is output in file "or"mypar.txt with the design
             double (*func)(double))    of the covariance matrix to be input.
 {  
   double ulim,u,r,q, dum;    Revision 1.89  2003/06/24 12:30:52  brouard
   double fu;    (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
   *fa=(*func)(*ax);    of the covariance matrix to be input.
   *fb=(*func)(*bx);  
   if (*fb > *fa) {    Revision 1.88  2003/06/23 17:54:56  brouard
     SHFT(dum,*ax,*bx,dum)    * 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.
       SHFT(dum,*fb,*fa,dum)  
       }    Revision 1.87  2003/06/18 12:26:01  brouard
   *cx=(*bx)+GOLD*(*bx-*ax);    Version 0.96
   *fc=(*func)(*cx);  
   while (*fb > *fc) {    Revision 1.86  2003/06/17 20:04:08  brouard
     r=(*bx-*ax)*(*fb-*fc);    (Module): Change position of html and gnuplot routines and added
     q=(*bx-*cx)*(*fb-*fa);    routine fileappend.
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    Revision 1.85  2003/06/17 13:12:43  brouard
     ulim=(*bx)+GLIMIT*(*cx-*bx);    * imach.c (Repository): Check when date of death was earlier that
     if ((*bx-u)*(u-*cx) > 0.0) {    current date of interview. It may happen when the death was just
       fu=(*func)(u);    prior to the death. In this case, dh was negative and likelihood
     } else if ((*cx-u)*(u-ulim) > 0.0) {    was wrong (infinity). We still send an "Error" but patch by
       fu=(*func)(u);    assuming that the date of death was just one stepm after the
       if (fu < *fc) {    interview.
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    (Repository): Because some people have very long ID (first column)
           SHFT(*fb,*fc,fu,(*func)(u))    we changed int to long in num[] and we added a new lvector for
           }    memory allocation. But we also truncated to 8 characters (left
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    truncation)
       u=ulim;    (Repository): No more line truncation errors.
       fu=(*func)(u);  
     } else {    Revision 1.84  2003/06/13 21:44:43  brouard
       u=(*cx)+GOLD*(*cx-*bx);    * imach.c (Repository): Replace "freqsummary" at a correct
       fu=(*func)(u);    place. It differs from routine "prevalence" which may be called
     }    many times. Probs is memory consuming and must be used with
     SHFT(*ax,*bx,*cx,u)    parcimony.
       SHFT(*fa,*fb,*fc,fu)    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       }  
 }    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 /*************** linmin ************************/  
     Revision 1.82  2003/06/05 15:57:20  brouard
 int ncom;    Add log in  imach.c and  fullversion number is now printed.
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  */
    /*
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))     Interpolated Markov Chain
 {  
   double brent(double ax, double bx, double cx,    Short summary of the programme:
                double (*f)(double), double tol, double *xmin);    
   double f1dim(double x);    This program computes Healthy Life Expectancies from
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
               double *fc, double (*func)(double));    first survey ("cross") where individuals from different ages are
   int j;    interviewed on their health status or degree of disability (in the
   double xx,xmin,bx,ax;    case of a health survey which is our main interest) -2- at least a
   double fx,fb,fa;    second wave of interviews ("longitudinal") which measure each change
      (if any) in individual health status.  Health expectancies are
   ncom=n;    computed from the time spent in each health state according to a
   pcom=vector(1,n);    model. More health states you consider, more time is necessary to reach the
   xicom=vector(1,n);    Maximum Likelihood of the parameters involved in the model.  The
   nrfunc=func;    simplest model is the multinomial logistic model where pij is the
   for (j=1;j<=n;j++) {    probability to be observed in state j at the second wave
     pcom[j]=p[j];    conditional to be observed in state i at the first wave. Therefore
     xicom[j]=xi[j];    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
   ax=0.0;    complex model than "constant and age", you should modify the program
   xx=1.0;    where the markup *Covariates have to be included here again* invites
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    you to do it.  More covariates you add, slower the
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    convergence.
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    The advantage of this computer programme, compared to a simple
 #endif    multinomial logistic model, is clear when the delay between waves is not
   for (j=1;j<=n;j++) {    identical for each individual. Also, if a individual missed an
     xi[j] *= xmin;    intermediate interview, the information is lost, but taken into
     p[j] += xi[j];    account using an interpolation or extrapolation.  
   }  
   free_vector(xicom,1,n);    hPijx is the probability to be observed in state i at age x+h
   free_vector(pcom,1,n);    conditional to the observed state i at age x. The delay 'h' can be
 }    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 /*************** powell ************************/    semester or year) is modelled as a multinomial logistic.  The hPx
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    matrix is simply the matrix product of nh*stepm elementary matrices
             double (*func)(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
   int i,ibig,j;    of the life expectancies. It also computes the period (stable) prevalence. 
   double del,t,*pt,*ptt,*xit;    
   double fp,fptt;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   double *xits;             Institut national d'études démographiques, Paris.
   pt=vector(1,n);    This software have been partly granted by Euro-REVES, a concerted action
   ptt=vector(1,n);    from the European Union.
   xit=vector(1,n);    It is copyrighted identically to a GNU software product, ie programme and
   xits=vector(1,n);    software can be distributed freely for non commercial use. Latest version
   *fret=(*func)(p);    can be accessed at http://euroreves.ined.fr/imach .
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     fp=(*fret);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     ibig=0;    
     del=0.0;    **********************************************************************/
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /*
     for (i=1;i<=n;i++)    main
       printf(" %d %.12f",i, p[i]);    read parameterfile
     printf("\n");    read datafile
     for (i=1;i<=n;i++) {    concatwav
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    freqsummary
       fptt=(*fret);    if (mle >= 1)
 #ifdef DEBUG      mlikeli
       printf("fret=%lf \n",*fret);    print results files
 #endif    if mle==1 
       printf("%d",i);fflush(stdout);       computes hessian
       linmin(p,xit,n,fret,func);    read end of parameter file: agemin, agemax, bage, fage, estepm
       if (fabs(fptt-(*fret)) > del) {        begin-prev-date,...
         del=fabs(fptt-(*fret));    open gnuplot file
         ibig=i;    open html file
       }    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 #ifdef DEBUG     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
       printf("%d %.12e",i,(*fret));                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       for (j=1;j<=n;j++) {      freexexit2 possible for memory heap.
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);    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
       for(j=1;j<=n;j++)         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
         printf(" p=%.12e",p[j]);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       printf("\n");  
 #endif         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
     }         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
 #ifdef DEBUG     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       int k[2],l;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       k[0]=1;  
       k[1]=-1;    forecasting if prevfcast==1 prevforecast call prevalence()
       printf("Max: %.12e",(*func)(p));    health expectancies
       for (j=1;j<=n;j++)    Variance-covariance of DFLE
         printf(" %.12e",p[j]);    prevalence()
       printf("\n");     movingaverage()
       for(l=0;l<=1;l++) {    varevsij() 
         for (j=1;j<=n;j++) {    if popbased==1 varevsij(,popbased)
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    total life expectancies
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    Variance of period (stable) prevalence
         }   end
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  */
       }  
 #endif  /* #define DEBUG */
   /* #define DEBUGBRENT */
   #define POWELL /* Instead of NLOPT */
       free_vector(xit,1,n);  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
       free_vector(xits,1,n);  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  #include <math.h>
       return;  #include <stdio.h>
     }  #include <stdlib.h>
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #include <string.h>
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  #ifdef _WIN32
       xit[j]=p[j]-pt[j];  #include <io.h>
       pt[j]=p[j];  #include <windows.h>
     }  #include <tchar.h>
     fptt=(*func)(ptt);  #else
     if (fptt < fp) {  #include <unistd.h>
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #endif
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  #include <limits.h>
         for (j=1;j<=n;j++) {  #include <sys/types.h>
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  #if defined(__GNUC__)
         }  #include <sys/utsname.h> /* Doesn't work on Windows */
 #ifdef DEBUG  #endif
         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++)  #include <sys/stat.h>
           printf(" %.12e",xit[j]);  #include <errno.h>
         printf("\n");  /* extern int errno; */
 #endif  
       }  /* #ifdef LINUX */
     }  /* #include <time.h> */
   }  /* #include "timeval.h" */
 }  /* #else */
   /* #include <sys/time.h> */
 /**** Prevalence limit ****************/  /* #endif */
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #include <time.h>
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #ifdef GSL
      matrix by transitions matrix until convergence is reached */  #include <gsl/gsl_errno.h>
   #include <gsl/gsl_multimin.h>
   int i, ii,j,k;  #endif
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  #ifdef NLOPT
   double **newm;  #include <nlopt.h>
   double agefin, delaymax=50 ; /* Max number of years to converge */  typedef struct {
     double (* function)(double [] );
   for (ii=1;ii<=nlstate+ndeath;ii++)  } myfunc_data ;
     for (j=1;j<=nlstate+ndeath;j++){  #endif
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
    cov[1]=1.;  
    #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #define GNUPLOTPROGRAM "gnuplot"
     newm=savm;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     /* Covariates have to be included here again */  #define FILENAMELENGTH 132
      cov[2]=agefin;  
    #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       for (k=1; k<=cptcovn;k++) {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
       }  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #define NINTERVMAX 8
       for (k=1; k<=cptcovprod;k++)  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   #define MAXN 20000
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  #define YEARM 12. /**< Number of months per year */
   #define AGESUP 130
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  #define AGEBASE 40
   #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
     savm=oldm;  #ifdef _WIN32
     oldm=newm;  #define DIRSEPARATOR '\\'
     maxmax=0.;  #define CHARSEPARATOR "\\"
     for(j=1;j<=nlstate;j++){  #define ODIRSEPARATOR '/'
       min=1.;  #else
       max=0.;  #define DIRSEPARATOR '/'
       for(i=1; i<=nlstate; i++) {  #define CHARSEPARATOR "/"
         sumnew=0;  #define ODIRSEPARATOR '\\'
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  #endif
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /* $Id$ */
         min=FMIN(min,prlim[i][j]);  /* $State$ */
       }  
       maxmin=max-min;  char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
       maxmax=FMAX(maxmax,maxmin);  char fullversion[]="$Revision$ $Date$"; 
     }  char strstart[80];
     if(maxmax < ftolpl){  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       return prlim;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     }  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
   }  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
 }  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
 /*************** transition probabilities **********/  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  int cptcovprodnoage=0; /**< Number of covariate products without age */   
 {  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   double s1, s2;  int cptcov=0; /* Working variable */
   /*double t34;*/  int npar=NPARMAX;
   int i,j,j1, nc, ii, jj;  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
     for(i=1; i<= nlstate; i++){  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     for(j=1; j<i;j++){  int popbased=0;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  int *wav; /* Number of waves for this individuual 0 is possible */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  int maxwav=0; /* Maxim number of waves */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       }  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       ps[i][j]=s2;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/                     to the likelihood and the sum of weights (done by funcone)*/
     }  int mle=1, weightopt=0;
     for(j=i+1; j<=nlstate+ndeath;j++){  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       }  int countcallfunc=0;  /* Count the number of calls to func */
       ps[i][j]=s2;  double jmean=1; /* Mean space between 2 waves */
     }  double **matprod2(); /* test */
   }  double **oldm, **newm, **savm; /* Working pointers to matrices */
   for(i=1; i<= nlstate; i++){  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
      s1=0;  /*FILE *fic ; */ /* Used in readdata only */
     for(j=1; j<i; j++)  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       s1+=exp(ps[i][j]);  FILE *ficlog, *ficrespow;
     for(j=i+1; j<=nlstate+ndeath; j++)  int globpr=0; /* Global variable for printing or not */
       s1+=exp(ps[i][j]);  double fretone; /* Only one call to likelihood */
     ps[i][i]=1./(s1+1.);  long ipmx=0; /* Number of contributions */
     for(j=1; j<i; j++)  double sw; /* Sum of weights */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  char filerespow[FILENAMELENGTH];
     for(j=i+1; j<=nlstate+ndeath; j++)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  FILE *ficresilk;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   } /* end i */  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  FILE *ficreseij;
     for(jj=1; jj<= nlstate+ndeath; jj++){  char filerese[FILENAMELENGTH];
       ps[ii][jj]=0;  FILE *ficresstdeij;
       ps[ii][ii]=1;  char fileresstde[FILENAMELENGTH];
     }  FILE *ficrescveij;
   }  char filerescve[FILENAMELENGTH];
   FILE  *ficresvij;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  char fileresv[FILENAMELENGTH];
     for(jj=1; jj<= nlstate+ndeath; jj++){  FILE  *ficresvpl;
      printf("%lf ",ps[ii][jj]);  char fileresvpl[FILENAMELENGTH];
    }  char title[MAXLINE];
     printf("\n ");  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     printf("\n ");printf("%lf ",cov[2]);*/  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 /*  char command[FILENAMELENGTH];
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  int  outcmd=0;
   goto end;*/  
     return ps;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 }  
   char filelog[FILENAMELENGTH]; /* Log file */
 /**************** Product of 2 matrices ******************/  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  char popfile[FILENAMELENGTH];
 {  
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
      before: only the contents of out is modified. The function returns  /* struct timezone tzp; */
      a pointer to pointers identical to out */  /* extern int gettimeofday(); */
   long i, j, k;  struct tm tml, *gmtime(), *localtime();
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  extern time_t time();
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   return out;  struct tm tm;
 }  
   char strcurr[80], strfor[80];
   
 /************* Higher Matrix Product ***************/  char *endptr;
   long lval;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double dval;
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  #define NR_END 1
      duration (i.e. until  #define FREE_ARG char*
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  #define FTOL 1.0e-10
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).  #define NRANSI 
      Model is determined by parameters x and covariates have to be  #define ITMAX 200 
      included manually here.  
   #define TOL 2.0e-4 
      */  
   #define CGOLD 0.3819660 
   int i, j, d, h, k;  #define ZEPS 1.0e-10 
   double **out, cov[NCOVMAX];  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   double **newm;  
   #define GOLD 1.618034 
   /* Hstepm could be zero and should return the unit matrix */  #define GLIMIT 100.0 
   for (i=1;i<=nlstate+ndeath;i++)  #define TINY 1.0e-20 
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  static double maxarg1,maxarg2;
       po[i][j][0]=(i==j ? 1.0 : 0.0);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    
   for(h=1; h <=nhstepm; h++){  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     for(d=1; d <=hstepm; d++){  #define rint(a) floor(a+0.5)
       newm=savm;  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
       /* Covariates have to be included here again */  #define mytinydouble 1.0e-16
       cov[1]=1.;  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /* static double dsqrarg; */
 for (k=1; k<=cptcovage;k++)  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  static double sqrarg;
    for (k=1; k<=cptcovprod;k++)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  int imx; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  int stepm=1;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /* Stepm, step in month: minimum step interpolation*/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  int estepm;
       oldm=newm;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     }  
     for(i=1; i<=nlstate+ndeath; i++)  int m,nb;
       for(j=1;j<=nlstate+ndeath;j++) {  long *num;
         po[i][j][h]=newm[i][j];  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
          */  double **pmmij, ***probs;
       }  double *ageexmed,*agecens;
   } /* end h */  double dateintmean=0;
   return po;  
 }  double *weight;
   int **s; /* Status */
   double *agedc;
 /*************** log-likelihood *************/  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
 double func( double *x)                    * covar=matrix(0,NCOVMAX,1,n); 
 {                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
   int i, ii, j, k, mi, d, kk;  double  idx; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   double **out;  int *Ndum; /** Freq of modality (tricode */
   double sw; /* Sum of weights */  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   double lli; /* Individual log likelihood */  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   long ipmx;  double *lsurv, *lpop, *tpop;
   /*extern weight */  
   /* We are differentiating ll according to initial status */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  double ftolhess; /**< Tolerance for computing hessian */
   /*for(i=1;i<imx;i++)  
 printf(" %d\n",s[4][i]);  /**************** split *************************/
   */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   cov[1]=1.;  {
     /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   for(k=1; k<=nlstate; k++) ll[k]=0.;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    */ 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    char  *ss;                            /* pointer */
        for(mi=1; mi<= wav[i]-1; mi++){    int   l1=0, l2=0;                             /* length counters */
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    l1 = strlen(path );                   /* length of path */
             for(d=0; d<dh[mi][i]; d++){    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
               newm=savm;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
               for (kk=1; kk<=cptcovage;kk++) {      strcpy( name, path );               /* we got the fullname name because no directory */
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
                  /*printf("%d %d",kk,Tage[kk]);*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
               }      /* get current working directory */
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/      /*    extern  char* getcwd ( char *buf , int len);*/
               /*cov[3]=pow(cov[2],2)/1000.;*/  #ifdef WIN32
       if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  #else
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          if (getcwd(dirc, FILENAME_MAX) == NULL) {
           savm=oldm;  #endif
           oldm=newm;        return( GLOCK_ERROR_GETCWD );
       }
       /* got dirc from getcwd*/
       } /* end mult */      printf(" DIRC = %s \n",dirc);
        } else {                              /* strip direcotry from path */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      ss++;                               /* after this, the filename */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      l2 = strlen( ss );                  /* length of filename */
       ipmx +=1;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       sw += weight[i];      strcpy( name, ss );         /* save file name */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     } /* end of wave */      dirc[l1-l2] = '\0';                 /* add zero */
   } /* end of individual */      printf(" DIRC2 = %s \n",dirc);
     }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* We add a separator at the end of dirc if not exists */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    l1 = strlen( dirc );                  /* length of directory */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    if( dirc[l1-1] != DIRSEPARATOR ){
   return -l;      dirc[l1] =  DIRSEPARATOR;
 }      dirc[l1+1] = 0; 
       printf(" DIRC3 = %s \n",dirc);
     }
 /*********** Maximum Likelihood Estimation ***************/    ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      ss++;
 {      strcpy(ext,ss);                     /* save extension */
   int i,j, iter;      l1= strlen( name);
   double **xi,*delti;      l2= strlen(ss)+1;
   double fret;      strncpy( finame, name, l1-l2);
   xi=matrix(1,npar,1,npar);      finame[l1-l2]= 0;
   for (i=1;i<=npar;i++)    }
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);    return( 0 );                          /* we're done */
   printf("Powell\n");  }
   powell(p,xi,npar,ftol,&iter,&fret,func);  
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  /******************************************/
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  
   void replace_back_to_slash(char *s, char*t)
 }  {
     int i;
 /**** Computes Hessian and covariance matrix ***/    int lg=0;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    i=0;
 {    lg=strlen(t);
   double  **a,**y,*x,pd;    for(i=0; i<= lg; i++) {
   double **hess;      (s[i] = t[i]);
   int i, j,jk;      if (t[i]== '\\') s[i]='/';
   int *indx;    }
   }
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  char *trimbb(char *out, char *in)
   void lubksb(double **a, int npar, int *indx, double b[]) ;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    char *s;
     s=out;
     while (*in != '\0'){
   hess=matrix(1,npar,1,npar);      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         in++;
   printf("\nCalculation of the hessian matrix. Wait...\n");      }
   for (i=1;i<=npar;i++){      *out++ = *in++;
     printf("%d",i);fflush(stdout);    }
     hess[i][i]=hessii(p,ftolhess,i,delti);    *out='\0';
     /*printf(" %f ",p[i]);*/    return s;
   }  }
   
   for (i=1;i<=npar;i++) {  /* char *substrchaine(char *out, char *in, char *chain) */
     for (j=1;j<=npar;j++)  {  /* { */
       if (j>i) {  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
         printf(".%d%d",i,j);fflush(stdout);  /*   char *s, *t; */
         hess[i][j]=hessij(p,delti,i,j);  /*   t=in;s=out; */
         hess[j][i]=hess[i][j];  /*   while ((*in != *chain) && (*in != '\0')){ */
       }  /*     *out++ = *in++; */
     }  /*   } */
   }  
   printf("\n");  /*   /\* *in matches *chain *\/ */
   /*   while ((*in++ == *chain++) && (*in != '\0')){ */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
    /*   } */
   a=matrix(1,npar,1,npar);  /*   in--; chain--; */
   y=matrix(1,npar,1,npar);  /*   while ( (*in != '\0')){ */
   x=vector(1,npar);  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   indx=ivector(1,npar);  /*     *out++ = *in++; */
   for (i=1;i<=npar;i++)  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*   } */
   ludcmp(a,npar,indx,&pd);  /*   *out='\0'; */
   /*   out=s; */
   for (j=1;j<=npar;j++) {  /*   return out; */
     for (i=1;i<=npar;i++) x[i]=0;  /* } */
     x[j]=1;  char *substrchaine(char *out, char *in, char *chain)
     lubksb(a,npar,indx,x);  {
     for (i=1;i<=npar;i++){    /* Substract chain 'chain' from 'in', return and output 'out' */
       matcov[i][j]=x[i];    /* in="V1+V1*age+age*age+V2", chain="age*age" */
     }  
   }    char *strloc;
   
   printf("\n#Hessian matrix#\n");    strcpy (out, in); 
   for (i=1;i<=npar;i++) {    strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
     for (j=1;j<=npar;j++) {    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
       printf("%.3e ",hess[i][j]);    if(strloc != NULL){ 
     }      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
     printf("\n");      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
   }      /* strcpy (strloc, strloc +strlen(chain));*/
     }
   /* Recompute Inverse */    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
   for (i=1;i<=npar;i++)    return out;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   
   /*  printf("\n#Hessian matrix recomputed#\n");  char *cutl(char *blocc, char *alocc, char *in, char occ)
   {
   for (j=1;j<=npar;j++) {    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
     for (i=1;i<=npar;i++) x[i]=0;       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     x[j]=1;       gives blocc="abcdef" and alocc="ghi2j".
     lubksb(a,npar,indx,x);       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     for (i=1;i<=npar;i++){    */
       y[i][j]=x[i];    char *s, *t;
       printf("%.3e ",y[i][j]);    t=in;s=in;
     }    while ((*in != occ) && (*in != '\0')){
     printf("\n");      *alocc++ = *in++;
   }    }
   */    if( *in == occ){
       *(alocc)='\0';
   free_matrix(a,1,npar,1,npar);      s=++in;
   free_matrix(y,1,npar,1,npar);    }
   free_vector(x,1,npar);   
   free_ivector(indx,1,npar);    if (s == t) {/* occ not found */
   free_matrix(hess,1,npar,1,npar);      *(alocc-(in-s))='\0';
       in=s;
     }
 }    while ( *in != '\0'){
       *blocc++ = *in++;
 /*************** hessian matrix ****************/    }
 double hessii( double x[], double delta, int theta, double delti[])  
 {    *blocc='\0';
   int i;    return t;
   int l=1, lmax=20;  }
   double k1,k2;  char *cutv(char *blocc, char *alocc, char *in, char occ)
   double p2[NPARMAX+1];  {
   double res;    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   double fx;       gives blocc="abcdef2ghi" and alocc="j".
   int k=0,kmax=10;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
   double l1;    */
     char *s, *t;
   fx=func(x);    t=in;s=in;
   for (i=1;i<=npar;i++) p2[i]=x[i];    while (*in != '\0'){
   for(l=0 ; l <=lmax; l++){      while( *in == occ){
     l1=pow(10,l);        *blocc++ = *in++;
     delts=delt;        s=in;
     for(k=1 ; k <kmax; k=k+1){      }
       delt = delta*(l1*k);      *blocc++ = *in++;
       p2[theta]=x[theta] +delt;    }
       k1=func(p2)-fx;    if (s == t) /* occ not found */
       p2[theta]=x[theta]-delt;      *(blocc-(in-s))='\0';
       k2=func(p2)-fx;    else
       /*res= (k1-2.0*fx+k2)/delt/delt; */      *(blocc-(in-s)-1)='\0';
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    in=s;
          while ( *in != '\0'){
 #ifdef DEBUG      *alocc++ = *in++;
       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){ */    *alocc='\0';
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    return s;
         k=kmax;  }
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  int nbocc(char *s, char occ)
         k=kmax; l=lmax*10.;  {
       }    int i,j=0;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    int lg=20;
         delts=delt;    i=0;
       }    lg=strlen(s);
     }    for(i=0; i<= lg; i++) {
   }    if  (s[i] == occ ) j++;
   delti[theta]=delts;    }
   return res;    return j;
    }
 }  
   /* void cutv(char *u,char *v, char*t, char occ) */
 double hessij( double x[], double delti[], int thetai,int thetaj)  /* { */
 {  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   int i;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   int l=1, l1, lmax=20;  /*      gives u="abcdef2ghi" and v="j" *\/ */
   double k1,k2,k3,k4,res,fx;  /*   int i,lg,j,p=0; */
   double p2[NPARMAX+1];  /*   i=0; */
   int k;  /*   lg=strlen(t); */
   /*   for(j=0; j<=lg-1; j++) { */
   fx=func(x);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   for (k=1; k<=2; k++) {  /*   } */
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  /*   for(j=0; j<p; j++) { */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*     (u[j] = t[j]); */
     k1=func(p2)-fx;  /*   } */
    /*      u[p]='\0'; */
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*    for(j=0; j<= lg; j++) { */
     k2=func(p2)-fx;  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
    /*   } */
     p2[thetai]=x[thetai]-delti[thetai]/k;  /* } */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  #ifdef _WIN32
    char * strsep(char **pp, const char *delim)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    char *p, *q;
     k4=func(p2)-fx;           
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    if ((p = *pp) == NULL)
 #ifdef DEBUG      return 0;
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    if ((q = strpbrk (p, delim)) != NULL)
 #endif    {
   }      *pp = q + 1;
   return res;      *q = '\0';
 }    }
     else
 /************** Inverse of matrix **************/      *pp = 0;
 void ludcmp(double **a, int n, int *indx, double *d)    return p;
 {  }
   int i,imax,j,k;  #endif
   double big,dum,sum,temp;  
   double *vv;  /********************** nrerror ********************/
    
   vv=vector(1,n);  void nrerror(char error_text[])
   *d=1.0;  {
   for (i=1;i<=n;i++) {    fprintf(stderr,"ERREUR ...\n");
     big=0.0;    fprintf(stderr,"%s\n",error_text);
     for (j=1;j<=n;j++)    exit(EXIT_FAILURE);
       if ((temp=fabs(a[i][j])) > big) big=temp;  }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  /*********************** vector *******************/
     vv[i]=1.0/big;  double *vector(int nl, int nh)
   }  {
   for (j=1;j<=n;j++) {    double *v;
     for (i=1;i<j;i++) {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       sum=a[i][j];    if (!v) nrerror("allocation failure in vector");
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    return v-nl+NR_END;
       a[i][j]=sum;  }
     }  
     big=0.0;  /************************ free vector ******************/
     for (i=j;i<=n;i++) {  void free_vector(double*v, int nl, int nh)
       sum=a[i][j];  {
       for (k=1;k<j;k++)    free((FREE_ARG)(v+nl-NR_END));
         sum -= a[i][k]*a[k][j];  }
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {  /************************ivector *******************************/
         big=dum;  int *ivector(long nl,long nh)
         imax=i;  {
       }    int *v;
     }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (j != imax) {    if (!v) nrerror("allocation failure in ivector");
       for (k=1;k<=n;k++) {    return v-nl+NR_END;
         dum=a[imax][k];  }
         a[imax][k]=a[j][k];  
         a[j][k]=dum;  /******************free ivector **************************/
       }  void free_ivector(int *v, long nl, long nh)
       *d = -(*d);  {
       vv[imax]=vv[j];    free((FREE_ARG)(v+nl-NR_END));
     }  }
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  /************************lvector *******************************/
     if (j != n) {  long *lvector(long nl,long nh)
       dum=1.0/(a[j][j]);  {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    long *v;
     }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   }    if (!v) nrerror("allocation failure in ivector");
   free_vector(vv,1,n);  /* Doesn't work */    return v-nl+NR_END;
 ;  }
 }  
   /******************free lvector **************************/
 void lubksb(double **a, int n, int *indx, double b[])  void free_lvector(long *v, long nl, long nh)
 {  {
   int i,ii=0,ip,j;    free((FREE_ARG)(v+nl-NR_END));
   double sum;  }
    
   for (i=1;i<=n;i++) {  /******************* imatrix *******************************/
     ip=indx[i];  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     sum=b[ip];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     b[ip]=b[i];  { 
     if (ii)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    int **m; 
     else if (sum) ii=i;    
     b[i]=sum;    /* allocate pointers to rows */ 
   }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   for (i=n;i>=1;i--) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
     sum=b[i];    m += NR_END; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    m -= nrl; 
     b[i]=sum/a[i][i];    
   }    
 }    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 /************ Frequencies ********************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)    m[nrl] += NR_END; 
 {  /* Some frequencies */    m[nrl] -= ncl; 
      
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   double ***freq; /* Frequencies */    
   double *pp;    /* return pointer to array of pointers to rows */ 
   double pos;    return m; 
   FILE *ficresp;  } 
   char fileresp[FILENAMELENGTH];  
   /****************** free_imatrix *************************/
   pp=vector(1,nlstate);  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
   strcpy(fileresp,"p");        long nch,ncl,nrh,nrl; 
   strcat(fileresp,fileres);       /* free an int matrix allocated by imatrix() */ 
   if((ficresp=fopen(fileresp,"w"))==NULL) {  { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     exit(0);    free((FREE_ARG) (m+nrl-NR_END)); 
   }  } 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
   j=cptcoveff;  {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
        j1++;    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
         for (i=-1; i<=nlstate+ndeath; i++)      m -= nrl;
          for (jk=-1; jk<=nlstate+ndeath; jk++)    
            for(m=agemin; m <= agemax+3; m++)    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
              freq[i][jk][m]=0;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
            m[nrl] += NR_END;
        for (i=1; i<=imx; i++) {    m[nrl] -= ncl;
          bool=1;  
          if  (cptcovn>0) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
            for (z1=1; z1<=cptcoveff; z1++)    return m;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
          }  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
           if (bool==1) {  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
            for(m=firstpass; m<=lastpass-1; m++){     */
              if(agev[m][i]==0) agev[m][i]=agemax+1;  }
              if(agev[m][i]==1) agev[m][i]=agemax+2;  
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*************************free matrix ************************/
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
            }  {
          }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
        }    free((FREE_ARG)(m+nrl-NR_END));
         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]]);  /******************* ma3x *******************************/
        }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
        fprintf(ficresp, "**********\n#");  {
        for(i=1; i<=nlstate;i++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double ***m;
        fprintf(ficresp, "\n");  
            m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for(i=(int)agemin; i <= (int)agemax+3; i++){    if (!m) nrerror("allocation failure 1 in matrix()");
     if(i==(int)agemax+3)    m += NR_END;
       printf("Total");    m -= nrl;
     else  
       printf("Age %d", i);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for(jk=1; jk <=nlstate ; jk++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    m[nrl] += NR_END;
         pp[jk] += freq[jk][m][i];    m[nrl] -= ncl;
     }  
     for(jk=1; jk <=nlstate ; jk++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       if(pp[jk]>=1.e-10)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    m[nrl][ncl] += NR_END;
       else    m[nrl][ncl] -= nll;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    for (j=ncl+1; j<=nch; j++) 
     }      m[nrl][j]=m[nrl][j-1]+nlay;
     for(jk=1; jk <=nlstate ; jk++){    
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    for (i=nrl+1; i<=nrh; i++) {
         pp[jk] += freq[jk][m][i];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     }      for (j=ncl+1; j<=nch; j++) 
     for(jk=1,pos=0; jk <=nlstate ; jk++)        m[i][j]=m[i][j-1]+nlay;
       pos += pp[jk];    }
     for(jk=1; jk <=nlstate ; jk++){    return m; 
       if(pos>=1.e-5)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       else    */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  }
       if( i <= (int) agemax){  
         if(pos>=1.e-5)  /*************************free ma3x ************************/
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       else  {
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
     for(jk=-1; jk <=nlstate+ndeath; jk++)  }
       for(m=-1; m <=nlstate+ndeath; m++)  
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  /*************** function subdirf ***********/
     if(i <= (int) agemax)  char *subdirf(char fileres[])
       fprintf(ficresp,"\n");  {
     printf("\n");    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/"); /* Add to the right */
  }    strcat(tmpout,fileres);
      return tmpout;
   fclose(ficresp);  }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
 }  /* End of Freq */  {
     
 /************* Waves Concatenation ***************/    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    strcat(tmpout,"/");
 {    strcat(tmpout,preop);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    strcat(tmpout,fileres);
      Death is a valid wave (if date is known).    return tmpout;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  }
      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.  /*************** function subdirf3 ***********/
      */  char *subdirf3(char fileres[], char *preop, char *preop2)
   {
   int i, mi, m;    
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* Caution optionfilefiname is hidden */
 float sum=0.;    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   for(i=1; i<=imx; i++){    strcat(tmpout,preop);
     mi=0;    strcat(tmpout,preop2);
     m=firstpass;    strcat(tmpout,fileres);
     while(s[m][i] <= nlstate){    return tmpout;
       if(s[m][i]>=1)  }
         mw[++mi][i]=m;  
       if(m >=lastpass)  char *asc_diff_time(long time_sec, char ascdiff[])
         break;  {
       else    long sec_left, days, hours, minutes;
         m++;    days = (time_sec) / (60*60*24);
     }/* end while */    sec_left = (time_sec) % (60*60*24);
     if (s[m][i] > nlstate){    hours = (sec_left) / (60*60) ;
       mi++;     /* Death is another wave */    sec_left = (sec_left) %(60*60);
       /* if(mi==0)  never been interviewed correctly before death */    minutes = (sec_left) /60;
          /* Only death is a correct wave */    sec_left = (sec_left) % (60);
       mw[mi][i]=m;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     }    return ascdiff;
   }
     wav[i]=mi;  
     if(mi==0)  /***************** f1dim *************************/
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  extern int ncom; 
   }  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
   for(i=1; i<=imx; i++){   
     for(mi=1; mi<wav[i];mi++){  double f1dim(double x) 
       if (stepm <=0)  { 
         dh[mi][i]=1;    int j; 
       else{    double f;
         if (s[mw[mi+1][i]][i] > nlstate) {    double *xt; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);   
           if(j=0) j=1;  /* Survives at least one month after exam */    xt=vector(1,ncom); 
         }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         else{    f=(*nrfunc)(xt); 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    free_vector(xt,1,ncom); 
           k=k+1;    return f; 
           if (j >= jmax) jmax=j;  } 
           else if (j <= jmin)jmin=j;  
           sum=sum+j;  /*****************brent *************************/
         }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         jk= j/stepm;  {
         jl= j -jk*stepm;    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
         ju= j -(jk+1)*stepm;     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
         if(jl <= -ju)     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
           dh[mi][i]=jk;     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
         else     * returned function value. 
           dh[mi][i]=jk+1;    */
         if(dh[mi][i]==0)    int iter; 
           dh[mi][i]=1; /* At least one step */    double a,b,d,etemp;
       }    double fu=0,fv,fw,fx;
     }    double ftemp=0.;
   }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    double e=0.0; 
 }   
 /*********** Tricode ****************************/    a=(ax < cx ? ax : cx); 
 void tricode(int *Tvar, int **nbcode, int imx)    b=(ax > cx ? ax : cx); 
 {    x=w=v=bx; 
   int Ndum[20],ij=1, k, j, i;    fw=fv=fx=(*f)(x); 
   int cptcode=0;    for (iter=1;iter<=ITMAX;iter++) { 
   cptcoveff=0;      xm=0.5*(a+b); 
        tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for (k=0; k<19; k++) Ndum[k]=0;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   for (k=1; k<=7; k++) ncodemax[k]=0;      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  #ifdef DEBUGBRENT
     for (i=1; i<=imx; i++) {      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       ij=(int)(covar[Tvar[j]][i]);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       Ndum[ij]++;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       if (ij > cptcode) cptcode=ij;  #endif
     }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/        return fx; 
     for (i=0; i<=cptcode; i++) {      } 
       if(Ndum[i]!=0) ncodemax[j]++;      ftemp=fu;
     }      if (fabs(e) > tol1) { 
     ij=1;        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
     for (i=1; i<=ncodemax[j]; i++) {        p=(x-v)*q-(x-w)*r; 
       for (k=0; k<=19; k++) {        q=2.0*(q-r); 
         if (Ndum[k] != 0) {        if (q > 0.0) p = -p; 
           nbcode[Tvar[j]][ij]=k;        q=fabs(q); 
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/        etemp=e; 
           ij++;        e=d; 
         }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         if (ij > ncodemax[j]) break;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }          else { 
     }          d=p/q; 
   }            u=x+d; 
  for (i=1; i<=10; i++) {          if (u-a < tol2 || b-u < tol2) 
       ij=Tvar[i];            d=SIGN(tol1,xm-x); 
       Ndum[ij]++;        } 
     }      } else { 
  ij=1;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
  for (i=1; i<=cptcovn; i++) {      } 
    if((Ndum[i]!=0) && (i<=ncov)){      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
      Tvaraff[i]=ij;      fu=(*f)(u); 
    ij++;      if (fu <= fx) { 
    }        if (u >= x) a=x; else b=x; 
  }        SHFT(v,w,x,u) 
          SHFT(fv,fw,fx,fu) 
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      } else { 
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];        if (u < x) a=u; else b=u; 
    /*printf("j=%d %d\n",j,Tvar[j]);*/        if (fu <= fw || w == x) { 
  }          v=w; 
            w=u; 
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);          fv=fw; 
     scanf("%d",i);*/          fw=fu; 
 }        } else if (fu <= fv || v == x || v == w) { 
           v=u; 
 /*********** Health Expectancies ****************/          fv=fu; 
         } 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      } 
 {    } 
   /* Health expectancies */    nrerror("Too many iterations in brent"); 
   int i, j, nhstepm, hstepm, h;    *xmin=x; 
   double age, agelim,hf;    return fx; 
   double ***p3mat;  } 
    
   fprintf(ficreseij,"# Health expectancies\n");  /****************** mnbrak ***********************/
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     for(j=1; j<=nlstate;j++)              double (*func)(double)) 
       fprintf(ficreseij," %1d-%1d",i,j);  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
   fprintf(ficreseij,"\n");  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
   hstepm=1*YEARM; /*  Every j years of age (in month) */  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */     */
     double ulim,u,r,q, dum;
   agelim=AGESUP;    double fu; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     /* nhstepm age range expressed in number of stepm */    double scale=10.;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    int iterscale=0;
     /* Typically if 20 years = 20*12/6=40 stepm */  
     if (stepm >= YEARM) hstepm=1;    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
     /*   *bx = *ax - (*ax - *bx)/scale; */
     /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
     for(i=1; i<=nlstate;i++)    /* } */
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    if (*fb > *fa) { 
           eij[i][j][(int)age] +=p3mat[i][j][h];      SHFT(dum,*ax,*bx,dum) 
         }      SHFT(dum,*fb,*fa,dum) 
        } 
     hf=1;    *cx=(*bx)+GOLD*(*bx-*ax); 
     if (stepm >= YEARM) hf=stepm/YEARM;    *fc=(*func)(*cx); 
     fprintf(ficreseij,"%.0f",age );  #ifdef DEBUG
     for(i=1; i<=nlstate;i++)    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
       for(j=1; j<=nlstate;j++){    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  #endif
       }    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
     fprintf(ficreseij,"\n");      r=(*bx-*ax)*(*fb-*fc); 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      q=(*bx-*cx)*(*fb-*fa); 
   }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
       ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
 /************ Variance ******************/      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
 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)        fu=(*func)(u); 
 {  #ifdef DEBUG
   /* Variance of health expectancies */        /* f(x)=A(x-u)**2+f(u) */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        double A, fparabu; 
   double **newm;        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
   double **dnewm,**doldm;        fparabu= *fa - A*(*ax-u)*(*ax-u);
   int i, j, nhstepm, hstepm, h;        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);
   int k, cptcode;        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);
    double *xp;        /* And thus,it can be that fu > *fc even if fparabu < *fc */
   double **gp, **gm;        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
   double ***gradg, ***trgradg;          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
   double ***p3mat;        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
   double age,agelim;  #endif 
   int theta;  #ifdef MNBRAKORIGINAL
   #else
    fprintf(ficresvij,"# Covariances of life expectancies\n");        if (fu > *fc) {
   fprintf(ficresvij,"# Age");  #ifdef DEBUG
   for(i=1; i<=nlstate;i++)        printf("mnbrak4  fu > fc \n");
     for(j=1; j<=nlstate;j++)        fprintf(ficlog, "mnbrak4 fu > fc\n");
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  #endif
   fprintf(ficresvij,"\n");          /* 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 *\/  */
           /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
   xp=vector(1,npar);          dum=u; /* Shifting c and u */
   dnewm=matrix(1,nlstate,1,npar);          u = *cx;
   doldm=matrix(1,nlstate,1,nlstate);          *cx = dum;
            dum = fu;
   hstepm=1*YEARM; /* Every year of age */          fu = *fc;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          *fc =dum;
   agelim = AGESUP;        } else { /* end */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #ifdef DEBUG
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        printf("mnbrak3  fu < fc \n");
     if (stepm >= YEARM) hstepm=1;        fprintf(ficlog, "mnbrak3 fu < fc\n");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  #endif
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          dum=u; /* Shifting c and u */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          u = *cx;
     gp=matrix(0,nhstepm,1,nlstate);          *cx = dum;
     gm=matrix(0,nhstepm,1,nlstate);          dum = fu;
           fu = *fc;
     for(theta=1; theta <=npar; theta++){          *fc =dum;
       for(i=1; i<=npar; i++){ /* Computes gradient */        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  #endif
       }      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #ifdef DEBUG
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        printf("mnbrak2  u after c but before ulim\n");
       for(j=1; j<= nlstate; j++){        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
         for(h=0; h<=nhstepm; h++){  #endif
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        fu=(*func)(u); 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        if (fu < *fc) { 
         }  #ifdef DEBUG
       }        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");
       for(i=1; i<=npar; i++) /* Computes gradient */  #endif
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            SHFT(*fb,*fc,fu,(*func)(u)) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } 
       for(j=1; j<= nlstate; j++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
         for(h=0; h<=nhstepm; h++){  #ifdef DEBUG
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
         }  #endif
       }        u=ulim; 
       for(j=1; j<= nlstate; j++)        fu=(*func)(u); 
         for(h=0; h<=nhstepm; h++){      } else { /* u could be left to b (if r > q parabola has a maximum) */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  #ifdef DEBUG
         }        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
     } /* End theta */        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
   #endif
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
     for(h=0; h<=nhstepm; h++)      } /* end tests */
       for(j=1; j<=nlstate;j++)      SHFT(*ax,*bx,*cx,u) 
         for(theta=1; theta <=npar; theta++)      SHFT(*fa,*fb,*fc,fu) 
           trgradg[h][j][theta]=gradg[h][theta][j];  #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=1;i<=nlstate;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);
       for(j=1;j<=nlstate;j++)  #endif
         vareij[i][j][(int)age] =0.;    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
     for(h=0;h<=nhstepm;h++){  } 
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  /*************** linmin ************************/
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         for(i=1;i<=nlstate;i++)  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
           for(j=1;j<=nlstate;j++)  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
             vareij[i][j][(int)age] += doldm[i][j];  the value of func at the returned location p . This is actually all accomplished by calling the
       }  routines mnbrak and brent .*/
     }  int ncom; 
     h=1;  double *pcom,*xicom;
     if (stepm >= YEARM) h=stepm/YEARM;  double (*nrfunc)(double []); 
     fprintf(ficresvij,"%.0f ",age );   
     for(i=1; i<=nlstate;i++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       for(j=1; j<=nlstate;j++){  { 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    double brent(double ax, double bx, double cx, 
       }                 double (*f)(double), double tol, double *xmin); 
     fprintf(ficresvij,"\n");    double f1dim(double x); 
     free_matrix(gp,0,nhstepm,1,nlstate);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     free_matrix(gm,0,nhstepm,1,nlstate);                double *fc, double (*func)(double)); 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    int j; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double xx,xmin,bx,ax; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double fx,fb,fa;
   } /* End age */  
      double scale=10., axs, xxs, xxss; /* Scale added for infinity */
   free_vector(xp,1,npar);   
   free_matrix(doldm,1,nlstate,1,npar);    ncom=n; 
   free_matrix(dnewm,1,nlstate,1,nlstate);    pcom=vector(1,n); 
     xicom=vector(1,n); 
 }    nrfunc=func; 
     for (j=1;j<=n;j++) { 
 /************ Variance of prevlim ******************/      pcom[j]=p[j]; 
 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)      xicom[j]=xi[j]; 
 {    } 
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    axs=0.0;
   double **newm;    xxss=1; /* 1 and using scale */
   double **dnewm,**doldm;    xxs=1;
   int i, j, nhstepm, hstepm;    do{
   int k, cptcode;      ax=0.;
   double *xp;      xx= xxs;
   double *gp, *gm;      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
   double **gradg, **trgradg;      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
   double age,agelim;      /* 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))   */
   int theta;      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
          /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
   fprintf(ficresvpl,"# Age");      /* 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]]*/
   for(i=1; i<=nlstate;i++)      if (fx != fx){
       fprintf(ficresvpl," %1d-%1d",i,i);          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
   fprintf(ficresvpl,"\n");          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);
       }
   xp=vector(1,npar);    }while(fx != fx);
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
      /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
   hstepm=1*YEARM; /* Every year of age */    /* fmin = f(p[j] + xmin * xi[j]) */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
   agelim = AGESUP;    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #ifdef DEBUG
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (stepm >= YEARM) hstepm=1;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  #endif
     gradg=matrix(1,npar,1,nlstate);    /* printf("linmin end "); */
     gp=vector(1,nlstate);    for (j=1;j<=n;j++) { 
     gm=vector(1,nlstate);      /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
       xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
     for(theta=1; theta <=npar; theta++){      /* if(xxs <1.0) */
       for(i=1; i<=npar; i++){ /* Computes gradient */      /*   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 ); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      p[j] += xi[j]; /* Parameters values are updated accordingly */
       }    } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* printf("\n"); */
       for(i=1;i<=nlstate;i++)    /* printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", *fret, (*func)(p)); */
         gp[i] = prlim[i][i];    free_vector(xicom,1,n); 
        free_vector(pcom,1,n); 
       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++)  /*************** powell ************************/
         gm[i] = prlim[i][i];  /*
   Minimization of a function func of n variables. Input consists of an initial starting point
       for(i=1;i<=nlstate;i++)  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
     } /* End theta */  such that failure to decrease by more than this amount on one iteration signals doneness. On
   output, p is set to the best point found, xi is the then-current direction set, fret is the returned
     trgradg =matrix(1,nlstate,1,npar);  function value at p , and iter is the number of iterations taken. The routine linmin is used.
    */
     for(j=1; j<=nlstate;j++)  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for(theta=1; theta <=npar; theta++)              double (*func)(double [])) 
         trgradg[j][theta]=gradg[theta][j];  { 
     void linmin(double p[], double xi[], int n, double *fret, 
     for(i=1;i<=nlstate;i++)                double (*func)(double [])); 
       varpl[i][(int)age] =0.;    int i,ibig,j; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    double del,t,*pt,*ptt,*xit;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    double directest;
     for(i=1;i<=nlstate;i++)    double fp,fptt;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    double *xits;
     int niterf, itmp;
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    pt=vector(1,n); 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    ptt=vector(1,n); 
     fprintf(ficresvpl,"\n");    xit=vector(1,n); 
     free_vector(gp,1,nlstate);    xits=vector(1,n); 
     free_vector(gm,1,nlstate);    *fret=(*func)(p); 
     free_matrix(gradg,1,npar,1,nlstate);    for (j=1;j<=n;j++) pt[j]=p[j]; 
     free_matrix(trgradg,1,nlstate,1,npar);      rcurr_time = time(NULL);  
   } /* End age */    for (*iter=1;;++(*iter)) { 
       fp=(*fret); /* From former iteration or initial value */
   free_vector(xp,1,npar);      ibig=0; 
   free_matrix(doldm,1,nlstate,1,npar);      del=0.0; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      rlast_time=rcurr_time;
       /* (void) gettimeofday(&curr_time,&tzp); */
 }      rcurr_time = time(NULL);  
       curr_time = *localtime(&rcurr_time);
       printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
 /***********************************************/  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
 /**************** Main Program *****************/     for (i=1;i<=n;i++) {
 /***********************************************/        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
 /*int main(int argc, char *argv[])*/        fprintf(ficrespow," %.12lf", p[i]);
 int main()      }
 {      printf("\n");
       fprintf(ficlog,"\n");
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;      fprintf(ficrespow,"\n");fflush(ficrespow);
   double agedeb, agefin,hf;      if(*iter <=3){
   double agemin=1.e20, agemax=-1.e20;        tml = *localtime(&rcurr_time);
         strcpy(strcurr,asctime(&tml));
   double fret;        rforecast_time=rcurr_time; 
   double **xi,tmp,delta;        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double dum; /* Dummy variable */          strcurr[itmp-1]='\0';
   double ***p3mat;        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   int *indx;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   char line[MAXLINE], linepar[MAXLINE];        for(niterf=10;niterf<=30;niterf+=10){
   char title[MAXLINE];          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          forecast_time = *localtime(&rforecast_time);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];          strcpy(strfor,asctime(&forecast_time));
   char filerest[FILENAMELENGTH];          itmp = strlen(strfor);
   char fileregp[FILENAMELENGTH];          if(strfor[itmp-1]=='\n')
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          strfor[itmp-1]='\0';
   int firstobs=1, lastobs=10;          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);
   int sdeb, sfin; /* Status at beginning and end */          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);
   int c,  h , cpt,l;        }
   int ju,jl, mi;      }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      for (i=1;i<=n;i++) { /* For each direction i */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
          fptt=(*fret); 
   int hstepm, nhstepm;  #ifdef DEBUG
   double bage, fage, age, agelim, agebase;            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   double ftolpl=FTOL;            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   double **prlim;  #endif
   double *severity;            printf("%d",i);fflush(stdout); /* print direction (parameter) i */
   double ***param; /* Matrix of parameters */        fprintf(ficlog,"%d",i);fflush(ficlog);
   double  *p;        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
   double **matcov; /* Matrix of covariance */                                      /* Outputs are fret(new point p) p is updated and xit rescaled */
   double ***delti3; /* Scale */        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
   double *delti; /* Scale */          /* because that direction will be replaced unless the gain del is small */
   double ***eij, ***vareij;          /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
   double **varpl; /* Variances of prevalence limits by age */          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
   double *epj, vepp;          /* with the new direction. */
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";          del=fabs(fptt-(*fret)); 
   char *alph[]={"a","a","b","c","d","e"}, str[4];          ibig=i; 
         } 
   char z[1]="c", occ;  #ifdef DEBUG
 #include <sys/time.h>        printf("%d %.12e",i,(*fret));
 #include <time.h>        fprintf(ficlog,"%d %.12e",i,(*fret));
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        for (j=1;j<=n;j++) {
   /* long total_usecs;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   struct timeval start_time, end_time;          printf(" x(%d)=%.12e",j,xit[j]);
            fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
         for(j=1;j<=n;j++) {
           printf(" p(%d)=%.12e",j,p[j]);
   printf("\nIMACH, Version 0.64a");          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
   printf("\nEnter the parameter file name: ");        }
         printf("\n");
 #ifdef windows        fprintf(ficlog,"\n");
   scanf("%s",pathtot);  #endif
   getcwd(pathcd, size);      } /* end loop on each direction i */
   /*cygwin_split_path(pathtot,path,optionfile);      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
   /* cutv(path,optionfile,pathtot,'\\');*/      /* 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? */
 split(pathtot, path,optionfile);        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
   chdir(path);        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
   replace(pathc,path);        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
 #endif        /* decreased of more than 3.84  */
 #ifdef unix        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
   scanf("%s",optionfile);        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
 #endif        /* By adding 10 parameters more the gain should be 18.31 */
   
 /*-------- arguments in the command line --------*/        /* Starting the program with initial values given by a former maximization will simply change */
         /* the scales of the directions and the directions, because the are reset to canonical directions */
   strcpy(fileres,"r");        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
   strcat(fileres, optionfile);        /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
   #ifdef DEBUG
   /*---------arguments file --------*/        int k[2],l;
         k[0]=1;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        k[1]=-1;
     printf("Problem with optionfile %s\n",optionfile);        printf("Max: %.12e",(*func)(p));
     goto end;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   }        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
   strcpy(filereso,"o");          fprintf(ficlog," %.12e",p[j]);
   strcat(filereso,fileres);        }
   if((ficparo=fopen(filereso,"w"))==NULL) {        printf("\n");
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        fprintf(ficlog,"\n");
   }        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
   /* Reads comments: lines beginning with '#' */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   while((c=getc(ficpar))=='#' && c!= EOF){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     ungetc(c,ficpar);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     fgets(line, MAXLINE, ficpar);          }
     puts(line);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     fputs(line,ficparo);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   }        }
   ungetc(c,ficpar);  #endif
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        free_vector(xit,1,n); 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   covar=matrix(0,NCOVMAX,1,n);            free_vector(pt,1,n); 
   if (strlen(model)<=1) cptcovn=0;        return; 
   else {      } 
     j=0;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     j=nbocc(model,'+');      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
     cptcovn=j+1;        ptt[j]=2.0*p[j]-pt[j]; 
   }        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
   ncovmodel=2+cptcovn;      } 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      fptt=(*func)(ptt); /* f_3 */
        if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   /* Read guess parameters */        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
   /* Reads comments: lines beginning with '#' */        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
   while((c=getc(ficpar))=='#' && c!= EOF){        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
     ungetc(c,ficpar);        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
     fgets(line, MAXLINE, ficpar);        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
     puts(line);        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
     fputs(line,ficparo);        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   }  #ifdef NRCORIGINAL
   ungetc(c,ficpar);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
    #else
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
     for(i=1; i <=nlstate; i++)        t= t- del*SQR(fp-fptt);
     for(j=1; j <=nlstate+ndeath-1; j++){  #endif
       fscanf(ficpar,"%1d%1d",&i1,&j1);        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
       fprintf(ficparo,"%1d%1d",i1,j1);  #ifdef DEBUG
       printf("%1d%1d",i,j);        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);
       for(k=1; k<=ncovmodel;k++){        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);
         fscanf(ficpar," %lf",&param[i][j][k]);        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
         printf(" %lf",param[i][j][k]);               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         fprintf(ficparo," %lf",param[i][j][k]);        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       }               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
       fscanf(ficpar,"\n");        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);
       printf("\n");        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
       fprintf(ficparo,"\n");  #endif
     }  #ifdef POWELLORIGINAL
          if (t < 0.0) { /* Then we use it for new direction */
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  #else
   p=param[1][1];        if (directest*t < 0.0) { /* Contradiction between both tests */
          printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
   /* Reads comments: lines beginning with '#' */        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
     ungetc(c,ficpar);        fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
     fgets(line, MAXLINE, ficpar);      } 
     puts(line);        if (directest < 0.0) { /* Then we use it for new direction */
     fputs(line,ficparo);  #endif
   }          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
   ungetc(c,ficpar);          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          }
   for(i=1; i <=nlstate; i++){          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     for(j=1; j <=nlstate+ndeath-1; j++){          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);  #ifdef DEBUG
       fprintf(ficparo,"%1d%1d",i1,j1);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for(k=1; k<=ncovmodel;k++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         fscanf(ficpar,"%le",&delti3[i][j][k]);          for(j=1;j<=n;j++){
         printf(" %le",delti3[i][j][k]);            printf(" %.12e",xit[j]);
         fprintf(ficparo," %le",delti3[i][j][k]);            fprintf(ficlog," %.12e",xit[j]);
       }          }
       fscanf(ficpar,"\n");          printf("\n");
       printf("\n");          fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");  #endif
     }        } /* end of t negative */
   }      } /* end if (fptt < fp)  */
   delti=delti3[1][1];    } 
    } 
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /**** Prevalence limit (stable or period prevalence)  ****************/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     puts(line);  {
     fputs(line,ficparo);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   }       matrix by transitions matrix until convergence is reached */
   ungetc(c,ficpar);    
      int i, ii,j,k;
   matcov=matrix(1,npar,1,npar);    double min, max, maxmin, maxmax,sumnew=0.;
   for(i=1; i <=npar; i++){    /* double **matprod2(); */ /* test */
     fscanf(ficpar,"%s",&str);    double **out, cov[NCOVMAX+1], **pmij();
     printf("%s",str);    double **newm;
     fprintf(ficparo,"%s",str);    double agefin, delaymax=50 ; /* Max number of years to converge */
     for(j=1; j <=i; j++){    
       fscanf(ficpar," %le",&matcov[i][j]);    for (ii=1;ii<=nlstate+ndeath;ii++)
       printf(" %.5le",matcov[i][j]);      for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficparo," %.5le",matcov[i][j]);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
     fscanf(ficpar,"\n");    
     printf("\n");    cov[1]=1.;
     fprintf(ficparo,"\n");    
   }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(i=1; i <=npar; i++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(j=i+1;j<=npar;j++)      newm=savm;
       matcov[i][j]=matcov[j][i];      /* Covariates have to be included here again */
          cov[2]=agefin;
   printf("\n");      if(nagesqr==1)
         cov[3]= agefin*agefin;;
       for (k=1; k<=cptcovn;k++) {
     /*-------- data file ----------*/        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     if((ficres =fopen(fileres,"w"))==NULL) {        /*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]]);*/
       printf("Problem with resultfile: %s\n", fileres);goto end;      }
     }      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     fprintf(ficres,"#%s\n",version);      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
          for (k=1; k<=cptcovprod;k++) /* Useless */
     if((fic=fopen(datafile,"r"))==NULL)    {        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       printf("Problem with datafile: %s\n", datafile);goto end;      
     }      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     n= lastobs;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     severity = vector(1,maxwav);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     outcome=imatrix(1,maxwav+1,1,n);      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
     num=ivector(1,n);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
     moisnais=vector(1,n);      
     annais=vector(1,n);      savm=oldm;
     moisdc=vector(1,n);      oldm=newm;
     andc=vector(1,n);      maxmax=0.;
     agedc=vector(1,n);      for(j=1;j<=nlstate;j++){
     cod=ivector(1,n);        min=1.;
     weight=vector(1,n);        max=0.;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for(i=1; i<=nlstate; i++) {
     mint=matrix(1,maxwav,1,n);          sumnew=0;
     anint=matrix(1,maxwav,1,n);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     s=imatrix(1,maxwav+1,1,n);          prlim[i][j]= newm[i][j]/(1-sumnew);
     adl=imatrix(1,maxwav+1,1,n);              /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
     tab=ivector(1,NCOVMAX);          max=FMAX(max,prlim[i][j]);
     ncodemax=ivector(1,8);          min=FMIN(min,prlim[i][j]);
         }
     i=1;        maxmin=max-min;
     while (fgets(line, MAXLINE, fic) != NULL)    {        maxmax=FMAX(maxmax,maxmin);
       if ((i >= firstobs) && (i <=lastobs)) {      } /* j loop */
              if(maxmax < ftolpl){
         for (j=maxwav;j>=1;j--){        return prlim;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      }
           strcpy(line,stra);    } /* age loop */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    return prlim; /* should not reach here */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  }
         }  
          /*************** transition probabilities ***************/ 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    /* According to parameters values stored in x and the covariate's values stored in cov,
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);       computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         for (j=ncov;j>=1;j--){       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);       ncth covariate in the global vector x is given by the formula:
         }       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
         num[i]=atol(stra);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
         /*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]));*/       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
        Outputs ps[i][j] the probability to be observed in j being in j according to
         i=i+1;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
       }    */
     }    double s1, lnpijopii;
     /*double t34;*/
     /*scanf("%d",i);*/    int i,j, nc, ii, jj;
   imx=i-1; /* Number of individuals */  
       for(i=1; i<= nlstate; i++){
   /* Calculation of the number of parameter from char model*/        for(j=1; j<i;j++){
   Tvar=ivector(1,15);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   Tprod=ivector(1,15);            /*lnpijopii += param[i][j][nc]*cov[nc];*/
   Tvaraff=ivector(1,15);            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   Tvard=imatrix(1,15,1,2);  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   Tage=ivector(1,15);                }
              ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   if (strlen(model) >1){  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     j=0, j1=0, k1=1, k2=1;        }
     j=nbocc(model,'+');        for(j=i+1; j<=nlstate+ndeath;j++){
     j1=nbocc(model,'*');          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     cptcovn=j+1;            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     cptcovprod=j1;            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
      /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     strcpy(modelsav,model);          }
    if (j==0) {          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       if (j1==0){        }
         cutv(stra,strb,modelsav,'V');      }
         Tvar[1]=atoi(strb);      
       }      for(i=1; i<= nlstate; i++){
       else if (j1==1) {        s1=0;
         cutv(stra,strb,modelsav,'*');        for(j=1; j<i; j++){
         Tage[1]=1; cptcovage++;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         if (strcmp(stra,"age")==0) {          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           cptcovprod--;        }
           cutv(strd,strc,strb,'V');        for(j=i+1; j<=nlstate+ndeath; j++){
           Tvar[1]=atoi(strc);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         else if (strcmp(strb,"age")==0) {        }
           cptcovprod--;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
           cutv(strd,strc,stra,'V');        ps[i][i]=1./(s1+1.);
           Tvar[1]=atoi(strc);        /* Computing other pijs */
         }        for(j=1; j<i; j++)
         else {          ps[i][j]= exp(ps[i][j])*ps[i][i];
           cutv(strd,strc,strb,'V');        for(j=i+1; j<=nlstate+ndeath; j++)
           cutv(stre,strd,stra,'V');          ps[i][j]= exp(ps[i][j])*ps[i][i];
           Tvar[1]=ncov+1;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
           for (k=1; k<=lastobs;k++)      } /* end i */
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];      
         }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         /*printf("%s %s %s\n", stra,strb,modelsav);        for(jj=1; jj<= nlstate+ndeath; jj++){
 printf("%d ",Tvar[1]);          ps[ii][jj]=0;
 scanf("%d",i);*/          ps[ii][ii]=1;
       }        }
     }      }
    else {      
       for(i=j; i>=1;i--){      
         cutv(stra,strb,modelsav,'+');      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         /*printf("%s %s %s\n", stra,strb,modelsav);      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           scanf("%d",i);*/      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         if (strchr(strb,'*')) {      /*   } */
           cutv(strd,strc,strb,'*');      /*   printf("\n "); */
           if (strcmp(strc,"age")==0) {      /* } */
             cptcovprod--;      /* printf("\n ");printf("%lf ",cov[2]);*/
             cutv(strb,stre,strd,'V');      /*
             Tvar[i+1]=atoi(stre);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
             cptcovage++;        goto end;*/
             Tage[cptcovage]=i+1;      return ps;
             printf("stre=%s ", stre);  }
           }  
           else if (strcmp(strd,"age")==0) {  /**************** Product of 2 matrices ******************/
             cptcovprod--;  
             cutv(strb,stre,strc,'V');  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
             Tvar[i+1]=atoi(stre);  {
             cptcovage++;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
             Tage[cptcovage]=i+1;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
           }    /* in, b, out are matrice of pointers which should have been initialized 
           else {       before: only the contents of out is modified. The function returns
             cutv(strb,stre,strc,'V');       a pointer to pointers identical to out */
             Tvar[i+1]=ncov+k1;    int i, j, k;
             cutv(strb,strc,strd,'V');    for(i=nrl; i<= nrh; i++)
             Tprod[k1]=i+1;      for(k=ncolol; k<=ncoloh; k++){
             Tvard[k1][1]=atoi(strc);        out[i][k]=0.;
             Tvard[k1][2]=atoi(stre);        for(j=ncl; j<=nch; j++)
             Tvar[cptcovn+k2]=Tvard[k1][1];          out[i][k] +=in[i][j]*b[j][k];
             Tvar[cptcovn+k2+1]=Tvard[k1][2];      }
             for (k=1; k<=lastobs;k++)    return out;
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  }
             k1++;  
             k2=k2+2;  
           }  /************* Higher Matrix Product ***************/
         }  
         else {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
           cutv(strd,strc,strb,'V');  {
           /* printf("%s %s %s", strd,strc,strb);*/    /* Computes the transition matrix starting at age 'age' over 
           Tvar[i+1]=atoi(strc);       'nhstepm*hstepm*stepm' months (i.e. until
         }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         strcpy(modelsav,stra);         nhstepm*hstepm matrices. 
       }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       cutv(strd,strc,stra,'V');       (typically every 2 years instead of every month which is too big 
       Tvar[1]=atoi(strc);       for the memory).
     }       Model is determined by parameters x and covariates have to be 
   }       included manually here. 
   /* for (i=1; i<=5; i++)  
      printf("i=%d %d ",i,Tvar[i]);*/       */
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/  
  /*printf("cptcovprod=%d ", cptcovprod);*/    int i, j, d, h, k;
   /*  scanf("%d ",i);*/    double **out, cov[NCOVMAX+1];
     fclose(fic);    double **newm;
     double agexact;
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/    /* Hstepm could be zero and should return the unit matrix */
       for(i=1;i<=n;i++) weight[i]=1.0;    for (i=1;i<=nlstate+ndeath;i++)
     }      for (j=1;j<=nlstate+ndeath;j++){
     /*-calculation of age at interview from date of interview and age at death -*/        oldm[i][j]=(i==j ? 1.0 : 0.0);
     agev=matrix(1,maxwav,1,imx);        po[i][j][0]=(i==j ? 1.0 : 0.0);
          }
     for (i=1; i<=imx; i++)  {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    for(h=1; h <=nhstepm; h++){
       for(m=1; (m<= maxwav); m++){      for(d=1; d <=hstepm; d++){
         if(s[m][i] >0){        newm=savm;
           if (s[m][i] == nlstate+1) {        /* Covariates have to be included here again */
             if(agedc[i]>0)        cov[1]=1.;
               if(moisdc[i]!=99 && andc[i]!=9999)        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
               agev[m][i]=agedc[i];        cov[2]=agexact;
             else{        if(nagesqr==1)
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          cov[3]= agexact*agexact;
               agev[m][i]=-1;        for (k=1; k<=cptcovn;k++) 
             }          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           }        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
           else if(s[m][i] !=9){ /* Should no more exist */          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
             if(mint[m][i]==99 || anint[m][i]==9999)        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
               agev[m][i]=1;          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             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);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
             }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
             else if(agev[m][i] >agemax){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
               agemax=agev[m][i];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        savm=oldm;
             }        oldm=newm;
             /*agev[m][i]=anint[m][i]-annais[i];*/      }
             /*   agev[m][i] = age[i]+2*m;*/      for(i=1; i<=nlstate+ndeath; i++)
           }        for(j=1;j<=nlstate+ndeath;j++) {
           else { /* =9 */          po[i][j][h]=newm[i][j];
             agev[m][i]=1;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
             s[m][i]=-1;        }
           }      /*printf("h=%d ",h);*/
         }    } /* end h */
         else /*= 0 Unknown */  /*     printf("\n H=%d \n",h); */
           agev[m][i]=1;    return po;
       }  }
      
     }  #ifdef NLOPT
     for (i=1; i<=imx; i++)  {    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
       for(m=1; (m<= maxwav); m++){    double fret;
         if (s[m][i] > (nlstate+ndeath)) {    double *xt;
           printf("Error: Wrong value in nlstate or ndeath\n");      int j;
           goto end;    myfunc_data *d2 = (myfunc_data *) pd;
         }  /* xt = (p1-1); */
       }    xt=vector(1,n); 
     }    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     free_vector(severity,1,maxwav);    printf("Function = %.12lf ",fret);
     free_imatrix(outcome,1,maxwav+1,1,n);    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     free_vector(moisnais,1,n);    printf("\n");
     free_vector(annais,1,n);   free_vector(xt,1,n);
     free_matrix(mint,1,maxwav,1,n);    return fret;
     free_matrix(anint,1,maxwav,1,n);  }
     free_vector(moisdc,1,n);  #endif
     free_vector(andc,1,n);  
   /*************** log-likelihood *************/
      double func( double *x)
     wav=ivector(1,imx);  {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    int i, ii, j, k, mi, d, kk;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
        double **out;
     /* Concatenates waves */    double sw; /* Sum of weights */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double lli; /* Individual log likelihood */
     int s1, s2;
     double bbh, survp;
       Tcode=ivector(1,100);    long ipmx;
       nbcode=imatrix(1,nvar,1,8);    double agexact;
       ncodemax[1]=1;    /*extern weight */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    /* We are differentiating ll according to initial status */
          /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
    codtab=imatrix(1,100,1,10);    /*for(i=1;i<imx;i++) 
    h=0;      printf(" %d\n",s[4][i]);
    m=pow(2,cptcoveff);    */
    
    for(k=1;k<=cptcoveff; k++){    ++countcallfunc;
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){    cov[1]=1.;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  
            h++;    for(k=1; k<=nlstate; k++) ll[k]=0.;
            if (h>m) h=1;codtab[h][k]=j;  
          }    if(mle==1){
        }      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[]
            Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
            to be observed in j being in i according to the model.
    /*for(i=1; i <=m ;i++){         */
      for(k=1; k <=cptcovn; k++){        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);            cov[2+nagesqr+k]=covar[Tvar[k]][i];
      }        }
      printf("\n");        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
    }           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
    scanf("%d",i);*/           has been calculated etc */
            for(mi=1; mi<= wav[i]-1; mi++){
    /* Calculates basic frequencies. Computes observed prevalence at single age          for (ii=1;ii<=nlstate+ndeath;ii++)
        and prints on file fileres'p'. */            for (j=1;j<=nlstate+ndeath;j++){
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(d=0; d<dh[mi][i]; d++){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            newm=savm;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            cov[2]=agexact;
                if(nagesqr==1)
     /* For Powell, parameters are in a vector p[] starting at p[1]              cov[3]= agexact*agexact;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            for (kk=1; kk<=cptcovage;kk++) {
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
             }
     if(mle==1){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
                oldm=newm;
     /*--------- results files --------------*/          } /* end mult */
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);        
              /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
    jk=1;          /* But now since version 0.9 we anticipate for bias at large stepm.
    fprintf(ficres,"# Parameters\n");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
    printf("# Parameters\n");           * (in months) between two waves is not a multiple of stepm, we rounded to 
    for(i=1,jk=1; i <=nlstate; i++){           * the nearest (and in case of equal distance, to the lowest) interval but now
      for(k=1; k <=(nlstate+ndeath); k++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
        if (k != i)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
          {           * probability in order to take into account the bias as a fraction of the way
            printf("%d%d ",i,k);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            fprintf(ficres,"%1d%1d ",i,k);           * -stepm/2 to stepm/2 .
            for(j=1; j <=ncovmodel; j++){           * For stepm=1 the results are the same as for previous versions of Imach.
              printf("%f ",p[jk]);           * For stepm > 1 the results are less biased than in previous versions. 
              fprintf(ficres,"%f ",p[jk]);           */
              jk++;          s1=s[mw[mi][i]][i];
            }          s2=s[mw[mi+1][i]][i];
            printf("\n");          bbh=(double)bh[mi][i]/(double)stepm; 
            fprintf(ficres,"\n");          /* bias bh is positive if real duration
          }           * is higher than the multiple of stepm and negative otherwise.
      }           */
    }          /* 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(mle==1){          if( s2 > nlstate){ 
     /* Computing hessian and covariance matrix */            /* i.e. if s2 is a death state and if the date of death is known 
     ftolhess=ftol; /* Usually correct */               then the contribution to the likelihood is the probability to 
     hesscov(matcov, p, npar, delti, ftolhess, func);               die between last step unit time and current  step unit time, 
  }               which is also equal to probability to die before dh 
     fprintf(ficres,"# Scales\n");               minus probability to die before dh-stepm . 
     printf("# Scales\n");               In version up to 0.92 likelihood was computed
      for(i=1,jk=1; i <=nlstate; i++){          as if date of death was unknown. Death was treated as any other
       for(j=1; j <=nlstate+ndeath; j++){          health state: the date of the interview describes the actual state
         if (j!=i) {          and not the date of a change in health state. The former idea was
           fprintf(ficres,"%1d%1d",i,j);          to consider that at each interview the state was recorded
           printf("%1d%1d",i,j);          (healthy, disable or death) and IMaCh was corrected; but when we
           for(k=1; k<=ncovmodel;k++){          introduced the exact date of death then we should have modified
             printf(" %.5e",delti[jk]);          the contribution of an exact death to the likelihood. This new
             fprintf(ficres," %.5e",delti[jk]);          contribution is smaller and very dependent of the step unit
             jk++;          stepm. It is no more the probability to die between last interview
           }          and month of death but the probability to survive from last
           printf("\n");          interview up to one month before death multiplied by the
           fprintf(ficres,"\n");          probability to die within a month. Thanks to Chris
         }          Jackson for correcting this bug.  Former versions increased
       }          mortality artificially. The bad side is that we add another loop
       }          which slows down the processing. The difference can be up to 10%
              lower mortality.
     k=1;            */
     fprintf(ficres,"# Covariance\n");          /* If, at the beginning of the maximization mostly, the
     printf("# Covariance\n");             cumulative probability or probability to be dead is
     for(i=1;i<=npar;i++){             constant (ie = 1) over time d, the difference is equal to
       /*  if (k>nlstate) k=1;             0.  out[s1][3] = savm[s1][3]: probability, being at state
       i1=(i-1)/(ncovmodel*nlstate)+1;             s1 at precedent wave, to be dead a month before current
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);             wave is equal to probability, being at state s1 at
       printf("%s%d%d",alph[k],i1,tab[i]);*/             precedent wave, to be dead at mont of the current
       fprintf(ficres,"%3d",i);             wave. Then the observed probability (that this person died)
       printf("%3d",i);             is null according to current estimated parameter. In fact,
       for(j=1; j<=i;j++){             it should be very low but not zero otherwise the log go to
         fprintf(ficres," %.5e",matcov[i][j]);             infinity.
         printf(" %.5e",matcov[i][j]);          */
       }  /* #ifdef INFINITYORIGINAL */
       fprintf(ficres,"\n");  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
       printf("\n");  /* #else */
       k++;  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
     }  /*          lli=log(mytinydouble); */
      /*        else */
     while((c=getc(ficpar))=='#' && c!= EOF){  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
       ungetc(c,ficpar);  /* #endif */
       fgets(line, MAXLINE, ficpar);              lli=log(out[s1][s2] - savm[s1][s2]);
       puts(line);  
       fputs(line,ficparo);          } else if  (s2==-2) {
     }            for (j=1,survp=0. ; j<=nlstate; j++) 
     ungetc(c,ficpar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
              /*survp += out[s1][j]; */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            lli= log(survp);
              }
     if (fage <= 2) {          
       bage = agemin;          else if  (s2==-4) { 
       fage = agemax;            for (j=3,survp=0. ; j<=nlstate; j++)  
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
     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\n",agemin,agemax,bage,fage);  
           else if  (s2==-5) { 
                for (j=1,survp=0. ; j<=2; j++)  
 /*------------ gnuplot -------------*/              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 chdir(pathcd);            lli= log(survp); 
   if((ficgp=fopen("graph.plt","w"))==NULL) {          } 
     printf("Problem with file graph.gp");goto end;          
   }          else{
 #ifdef windows            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fprintf(ficgp,"cd \"%s\" \n",pathc);            /*  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 */
 #endif          } 
 m=pow(2,cptcoveff);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
  /* 1eme*/          /*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); */
   for (cpt=1; cpt<= nlstate ; cpt ++) {          ipmx +=1;
    for (k1=1; k1<= m ; k1 ++) {          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 #ifdef windows          /* if (lli < log(mytinydouble)){ */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);          /*   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); */
 #endif          /*   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]); */
 #ifdef unix          /* } */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        } /* end of wave */
 #endif      } /* end of individual */
     }  else if(mle==2){
 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\"Stationary prevalence\" w l 0,\"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\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            newm=savm;
      for (i=1; i<= nlstate ; i ++) {            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            cov[2]=agexact;
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if(nagesqr==1)
 }                cov[3]= agexact*agexact;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            for (kk=1; kk<=cptcovage;kk++) {
 #ifdef unix              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
 fprintf(ficgp,"\nset ter gif small size 400,300");            }
 #endif            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    }            savm=oldm;
   }            oldm=newm;
   /*2 eme*/          } /* end mult */
         
   for (k1=1; k1<= m ; k1 ++) {          s1=s[mw[mi][i]][i];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          s2=s[mw[mi+1][i]][i];
              bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1; i<= nlstate+1 ; i ++) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       k=2*i;          ipmx +=1;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          sw += weight[i];
       for (j=1; j<= nlstate+1 ; j ++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        } /* end of wave */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      } /* end of individual */
 }      }  else if(mle==3){  /* exponential inter-extrapolation */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(mi=1; mi<= wav[i]-1; mi++){
       for (j=1; j<= nlstate+1 ; j ++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for (j=1;j<=nlstate+ndeath;j++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }                savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficgp,"\" t\"\" w l 0,");            }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          for(d=0; d<dh[mi][i]; d++){
       for (j=1; j<= nlstate+1 ; j ++) {            newm=savm;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   else fprintf(ficgp," \%%*lf (\%%*lf)");            cov[2]=agexact;
 }              if(nagesqr==1)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              cov[3]= agexact*agexact;
       else fprintf(ficgp,"\" t\"\" w l 0,");            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            }
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /*3eme*/            savm=oldm;
             oldm=newm;
   for (k1=1; k1<= m ; k1 ++) {          } /* end mult */
     for (cpt=1; cpt<= nlstate ; cpt ++) {        
       k=2+nlstate*(cpt-1);          s1=s[mw[mi][i]][i];
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          s2=s[mw[mi+1][i]][i];
       for (i=1; i< nlstate ; i ++) {          bbh=(double)bh[mi][i]/(double)stepm; 
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          lli= (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;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
        } /* end of individual */
   /* CV preval stat */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   for (k1=1; k1<= m ; k1 ++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (cpt=1; cpt<nlstate ; cpt ++) {        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       k=3;        for(mi=1; mi<= wav[i]-1; mi++){
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (i=1; i< nlstate ; i ++)            for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficgp,"+$%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++) {
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
     }            }
   }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* proba elementaires */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    for(i=1,jk=1; i <=nlstate; i++){            savm=oldm;
     for(k=1; k <=(nlstate+ndeath); k++){            oldm=newm;
       if (k != i) {          } /* end mult */
         for(j=1; j <=ncovmodel; j++){        
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/          s1=s[mw[mi][i]][i];
           /*fprintf(ficgp,"%s",alph[1]);*/          s2=s[mw[mi+1][i]][i];
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          if( s2 > nlstate){ 
           jk++;            lli=log(out[s1][s2] - savm[s1][s2]);
           fprintf(ficgp,"\n");          }else{
         }            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;
   for(jk=1; jk <=m; jk++) {  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);        } /* end of wave */
    i=1;      } /* end of individual */
    for(k2=1; k2<=nlstate; k2++) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
      k3=i;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      for(k=1; k<=(nlstate+ndeath); k++) {        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
        if (k != k2){        for(mi=1; mi<= wav[i]-1; mi++){
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          for (ii=1;ii<=nlstate+ndeath;ii++)
 ij=1;            for (j=1;j<=nlstate+ndeath;j++){
         for(j=3; j <=ncovmodel; j++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            }
             ij++;          for(d=0; d<dh[mi][i]; d++){
           }            newm=savm;
           else            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            cov[2]=agexact;
         }            if(nagesqr==1)
           fprintf(ficgp,")/(1");              cov[3]= agexact*agexact;
                    for (kk=1; kk<=cptcovage;kk++) {
         for(k1=1; k1 <=nlstate; k1++){                cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            }
 ij=1;          
           for(j=3; j <=ncovmodel; j++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            savm=oldm;
             ij++;            oldm=newm;
           }          } /* end mult */
           else        
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          s1=s[mw[mi][i]][i];
           }          s2=s[mw[mi+1][i]][i];
           fprintf(ficgp,")");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          ipmx +=1;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          sw += weight[i];
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         i=i+ncovmodel;          /*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 */
      }      } /* end of individual */
    }    } /* End of if */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
        l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fclose(ficgp);    return -l;
      }
 chdir(path);  
     free_matrix(agev,1,maxwav,1,imx);  /*************** log-likelihood *************/
     free_ivector(wav,1,imx);  double funcone( double *x)
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  {
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    /* Same as likeli but slower because of a lot of printf and if */
        int i, ii, j, k, mi, d, kk;
     free_imatrix(s,1,maxwav+1,1,n);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
        double **out;
        double lli; /* Individual log likelihood */
     free_ivector(num,1,n);    double llt;
     free_vector(agedc,1,n);    int s1, s2;
     free_vector(weight,1,n);    double bbh, survp;
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    double agexact;
     fclose(ficparo);    /*extern weight */
     fclose(ficres);    /* We are differentiating ll according to initial status */
     /*  }*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        /*for(i=1;i<imx;i++) 
    /*________fin mle=1_________*/      printf(" %d\n",s[4][i]);
        */
     cov[1]=1.;
    
     /* No more information from the sample is required now */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     ungetc(c,ficpar);      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
     fgets(line, MAXLINE, ficpar);      for(mi=1; mi<= wav[i]-1; mi++){
     puts(line);        for (ii=1;ii<=nlstate+ndeath;ii++)
     fputs(line,ficparo);          for (j=1;j<=nlstate+ndeath;j++){
   }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   ungetc(c,ficpar);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
            }
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        for(d=0; d<dh[mi][i]; d++){
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          newm=savm;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /*--------- index.htm --------*/          cov[2]=agexact;
           if(nagesqr==1)
   if((fichtm=fopen("index.htm","w"))==NULL)    {            cov[3]= agexact*agexact;
     printf("Problem with index.htm \n");goto end;          for (kk=1; kk<=cptcovage;kk++) {
   }            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           }
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          savm=oldm;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          oldm=newm;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>        } /* end mult */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        
         s1=s[mw[mi][i]][i];
  fprintf(fichtm," <li>Graphs</li>\n<p>");        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
  m=cptcoveff;        /* bias is positive if real duration
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}         * is higher than the multiple of stepm and negative otherwise.
          */
  j1=0;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
  for(k1=1; k1<=m;k1++){          lli=log(out[s1][s2] - savm[s1][s2]);
    for(i1=1; i1<=ncodemax[k1];i1++){        } else if  (s2==-2) {
        j1++;          for (j=1,survp=0. ; j<=nlstate; j++) 
        if (cptcovn > 0) {            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
          fprintf(fichtm,"<hr>************ Results for covariates");          lli= log(survp);
          for (cpt=1; cpt<=cptcoveff;cpt++)        }else if (mle==1){
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          fprintf(fichtm," ************\n<hr>");        } 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 */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        } else if(mle==3){  /* exponential inter-extrapolation */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
        for(cpt=1; cpt<nlstate;cpt++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          lli=log(out[s1][s2]); /* Original formula */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        } else{  /* mle=0 back to 1 */
        }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for(cpt=1; cpt<=nlstate;cpt++) {          /*lli=log(out[s1][s2]); */ /* Original formula */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        } /* End of if */
 interval) in state (%d): v%s%d%d.gif <br>        ipmx +=1;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          sw += weight[i];
      }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      for(cpt=1; cpt<=nlstate;cpt++) {        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        if(globpr){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
      }   %11.6f %11.6f %11.6f ", \
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 health expectancies in states (1) and (2): e%s%d.gif<br>                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
 fprintf(fichtm,"\n</body>");            llt +=ll[k]*gipmx/gsw;
    }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
  }          }
 fclose(fichtm);          fprintf(ficresilk," %10.6f\n", -llt);
         }
   /*--------------- Prevalence limit --------------*/      } /* end of wave */
      } /* end of individual */
   strcpy(filerespl,"pl");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   strcat(filerespl,fileres);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    if(globpr==0){ /* First time we count the contributions and weights */
   }      gipmx=ipmx;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      gsw=sw;
   fprintf(ficrespl,"#Prevalence limit\n");    }
   fprintf(ficrespl,"#Age ");    return -l;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  }
   fprintf(ficrespl,"\n");  
    
   prlim=matrix(1,nlstate,1,nlstate);  /*************** function likelione ***********/
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  {
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* This routine should help understanding what is done with 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       the selection of individuals/waves and
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       to check the exact contribution to the likelihood.
   k=0;       Plotting could be done.
   agebase=agemin;     */
   agelim=agemax;    int k;
   ftolpl=1.e-10;  
   i1=cptcoveff;    if(*globpri !=0){ /* Just counts and sums, no printings */
   if (cptcovn < 1){i1=1;}      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
   for(cptcov=1;cptcov<=i1;cptcov++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        printf("Problem with resultfile: %s\n", fileresilk);
         k=k+1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      }
         fprintf(ficrespl,"\n#******");      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");
         for(j=1;j<=cptcoveff;j++)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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(ficrespl,"******\n");      for(k=1; k<=nlstate; k++) 
                fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         for (age=agebase; age<=agelim; age++){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    }
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    *fretone=(*funcone)(p);
           fprintf(ficrespl," %.5f", prlim[i][i]);    if(*globpri !=0){
           fprintf(ficrespl,"\n");      fclose(ficresilk);
         }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       }      fflush(fichtm); 
     }    } 
   fclose(ficrespl);    return;
   /*------------- h Pij x at various ages ------------*/  }
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  /*********** Maximum Likelihood Estimation ***************/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   printf("Computing pij: result on file '%s' \n", filerespij);  {
      int i,j, iter=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double **xi;
   if (stepm<=24) stepsize=2;    double fret;
     double fretone; /* Only one call to likelihood */
   agelim=AGESUP;    /*  char filerespow[FILENAMELENGTH];*/
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  #ifdef NLOPT
      int creturn;
   k=0;    nlopt_opt opt;
   for(cptcov=1;cptcov<=i1;cptcov++){    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double *lb;
       k=k+1;    double minf; /* the minimum objective value, upon return */
         fprintf(ficrespij,"\n#****** ");    double * p1; /* Shifted parameters from 0 instead of 1 */
         for(j=1;j<=cptcoveff;j++)    myfunc_data dinst, *d = &dinst;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  #endif
         fprintf(ficrespij,"******\n");  
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    xi=matrix(1,npar,1,npar);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for (i=1;i<=npar;i++)
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (j=1;j<=npar;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        xi[i][j]=(i==j ? 1.0 : 0.0);
           oldm=oldms;savm=savms;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      strcpy(filerespow,"pow"); 
           fprintf(ficrespij,"# Age");    strcat(filerespow,fileres);
           for(i=1; i<=nlstate;i++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
             for(j=1; j<=nlstate+ndeath;j++)      printf("Problem with resultfile: %s\n", filerespow);
               fprintf(ficrespij," %1d-%1d",i,j);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
           fprintf(ficrespij,"\n");    }
           for (h=0; h<=nhstepm; h++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    for (i=1;i<=nlstate;i++)
             for(i=1; i<=nlstate;i++)      for(j=1;j<=nlstate+ndeath;j++)
               for(j=1; j<=nlstate+ndeath;j++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fprintf(ficrespow,"\n");
             fprintf(ficrespij,"\n");  #ifdef POWELL
           }    powell(p,xi,npar,ftol,&iter,&fret,func);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #endif
           fprintf(ficrespij,"\n");  
         }  #ifdef NLOPT
     }  #ifdef NEWUOA
   }    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
   fclose(ficrespij);    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
   /*---------- Health expectancies and variances ------------*/    lb=vector(0,npar-1);
     for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   strcpy(filerest,"t");    nlopt_set_lower_bounds(opt, lb);
   strcat(filerest,fileres);    nlopt_set_initial_step1(opt, 0.1);
   if((ficrest=fopen(filerest,"w"))==NULL) {    
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   }    d->function = func;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     nlopt_set_min_objective(opt, myfunc, d);
     nlopt_set_xtol_rel(opt, ftol);
   strcpy(filerese,"e");    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
   strcat(filerese,fileres);      printf("nlopt failed! %d\n",creturn); 
   if((ficreseij=fopen(filerese,"w"))==NULL) {    }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    else {
   }      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
  strcpy(fileresv,"v");    }
   strcat(fileresv,fileres);    nlopt_destroy(opt);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  #endif
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    free_matrix(xi,1,npar,1,npar);
   }    fclose(ficrespow);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    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));
   k=0;    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  }
       k=k+1;  
       fprintf(ficrest,"\n#****** ");  /**** Computes Hessian and covariance matrix ***/
       for(j=1;j<=cptcoveff;j++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  {
       fprintf(ficrest,"******\n");    double  **a,**y,*x,pd;
     double **hess;
       fprintf(ficreseij,"\n#****** ");    int i, j;
       for(j=1;j<=cptcoveff;j++)    int *indx;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    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);
       fprintf(ficresvij,"\n#****** ");    void lubksb(double **a, int npar, int *indx, double b[]) ;
       for(j=1;j<=cptcoveff;j++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    double gompertz(double p[]);
       fprintf(ficresvij,"******\n");    hess=matrix(1,npar,1,npar);
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    printf("\nCalculation of the hessian matrix. Wait...\n");
       oldm=oldms;savm=savms;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      for (i=1;i<=npar;i++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      printf("%d",i);fflush(stdout);
       oldm=oldms;savm=savms;      fprintf(ficlog,"%d",i);fflush(ficlog);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     
             hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      /*  printf(" %f ",p[i]);
       fprintf(ficrest,"\n");          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
            }
       hf=1;    
       if (stepm >= YEARM) hf=stepm/YEARM;    for (i=1;i<=npar;i++) {
       epj=vector(1,nlstate+1);      for (j=1;j<=npar;j++)  {
       for(age=bage; age <=fage ;age++){        if (j>i) { 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          printf(".%d%d",i,j);fflush(stdout);
         fprintf(ficrest," %.0f",age);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          hess[i][j]=hessij(p,delti,i,j,func,npar);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];          hess[j][i]=hess[i][j];    
           }          /*printf(" %lf ",hess[i][j]);*/
           epj[nlstate+1] +=epj[j];        }
         }      }
         for(i=1, vepp=0.;i <=nlstate;i++)    }
           for(j=1;j <=nlstate;j++)    printf("\n");
             vepp += vareij[i][j][(int)age];    fprintf(ficlog,"\n");
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  
         for(j=1;j <=nlstate;j++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         }    
         fprintf(ficrest,"\n");    a=matrix(1,npar,1,npar);
       }    y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
   }    indx=ivector(1,npar);
            for (i=1;i<=npar;i++)
  fclose(ficreseij);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
  fclose(ficresvij);    ludcmp(a,npar,indx,&pd);
   fclose(ficrest);  
   fclose(ficpar);    for (j=1;j<=npar;j++) {
   free_vector(epj,1,nlstate+1);      for (i=1;i<=npar;i++) x[i]=0;
   /*  scanf("%d ",i); */      x[j]=1;
       lubksb(a,npar,indx,x);
   /*------- Variance limit prevalence------*/        for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
 strcpy(fileresvpl,"vpl");      }
   strcat(fileresvpl,fileres);    }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    printf("\n#Hessian matrix#\n");
     exit(0);    fprintf(ficlog,"\n#Hessian matrix#\n");
   }    for (i=1;i<=npar;i++) { 
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
  k=0;        fprintf(ficlog,"%.3e ",hess[i][j]);
  for(cptcov=1;cptcov<=i1;cptcov++){      }
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf("\n");
      k=k+1;      fprintf(ficlog,"\n");
      fprintf(ficresvpl,"\n#****** ");    }
      for(j=1;j<=cptcoveff;j++)  
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* Recompute Inverse */
      fprintf(ficresvpl,"******\n");    for (i=1;i<=npar;i++)
            for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    ludcmp(a,npar,indx,&pd);
      oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    /*  printf("\n#Hessian matrix recomputed#\n");
    }  
  }    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   fclose(ficresvpl);      x[j]=1;
       lubksb(a,npar,indx,x);
   /*---------- End : free ----------------*/      for (i=1;i<=npar;i++){ 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        y[i][j]=x[i];
          printf("%.3e ",y[i][j]);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        fprintf(ficlog,"%.3e ",y[i][j]);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      }
        printf("\n");
        fprintf(ficlog,"\n");
   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(a,1,npar,1,npar);
      free_matrix(y,1,npar,1,npar);
   free_matrix(matcov,1,npar,1,npar);    free_vector(x,1,npar);
   free_vector(delti,1,npar);    free_ivector(indx,1,npar);
      free_matrix(hess,1,npar,1,npar);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
   
   printf("End of Imach\n");  }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
    /*************** hessian matrix ****************/
   /* 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);*/  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   /*printf("Total time was %d uSec.\n", total_usecs);*/  {
   /*------ End -----------*/    int i;
     int l=1, lmax=20;
  end:    double k1,k2;
 #ifdef windows    double p2[MAXPARM+1]; /* identical to x */
  chdir(pathcd);    double res;
 #endif    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
  system("wgnuplot graph.plt");    double fx;
     int k=0,kmax=10;
 #ifdef windows    double l1;
   while (z[0] != 'q') {  
     chdir(pathcd);    fx=func(x);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    for (i=1;i<=npar;i++) p2[i]=x[i];
     scanf("%s",z);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
     if (z[0] == 'c') system("./imach");      l1=pow(10,l);
     else if (z[0] == 'e') {      delts=delt;
       chdir(path);      for(k=1 ; k <kmax; k=k+1){
       system("index.htm");        delt = delta*(l1*k);
     }        p2[theta]=x[theta] +delt;
     else if (z[0] == 'q') exit(0);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   }        p2[theta]=x[theta]-delt;
 #endif        k2=func(p2)-fx;
 }        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   #ifdef DEBUGHESS
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
         }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10;
         }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
         }
       }
     }
     delti[theta]=delts;
     return res; 
     
   }
   
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
     int i;
     int l=1, lmax=20;
     double k1,k2,k3,k4,res,fx;
     double p2[MAXPARM+1];
     int k;
   
     fx=func(x);
     for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
     
       p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     
       p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
     
       p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
     }
     return res;
   }
   
   /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   { 
     int i,imax,j,k; 
     double big,dum,sum,temp; 
     double *vv; 
    
     vv=vector(1,n); 
     *d=1.0; 
     for (i=1;i<=n;i++) { 
       big=0.0; 
       for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
     } 
     for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
         sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
       } 
       big=0.0; 
       for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
         for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
           imax=i; 
         } 
       } 
       if (j != imax) { 
         for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
         } 
         *d = -(*d); 
         vv[imax]=vv[j]; 
       } 
       indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
         dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
     } 
     free_vector(vv,1,n);  /* Doesn't work */
   ;
   } 
   
   void lubksb(double **a, int n, int *indx, double b[]) 
   { 
     int i,ii=0,ip,j; 
     double sum; 
    
     for (i=1;i<=n;i++) { 
       ip=indx[i]; 
       sum=b[ip]; 
       b[ip]=b[i]; 
       if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
       b[i]=sum; 
     } 
     for (i=n;i>=1;i--) { 
       sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
     } 
   } 
   
   void pstamp(FILE *fichier)
   {
     fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
   
   /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   {  /* Some frequencies */
     
     int i, m, jk, j1, bool, z1,j;
     int first;
     double ***freq; /* Frequencies */
     double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
     
     pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
     strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
     }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
     
     j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
     first=1;
   
     /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
     /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
     /*    j1++; */
     for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
         
         for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
         
         dateintsum=0;
         k2cpt=0;
         for (i=1; i<=imx; i++) {
           bool=1;
           if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
             for (z1=1; z1<=cptcoveff; z1++)       
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                   /* Tests if the value of each of the covariates of i is equal to filter j1 */
                 bool=0;
                 /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
                   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                   j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
                 /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
               } 
           }
    
           if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 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];
                 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];
                 }
                 
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
                   k2cpt++;
                 }
                 /*}*/
             }
           }
         } /* end i */
          
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         pstamp(ficresp);
         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]]);
           fprintf(ficresp, "**********\n#");
           fprintf(ficlog, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficlog, "**********\n#");
         }
         for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
         
         for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
             fprintf(ficlog,"Total");
           }else{
             if(first==1){
               first=0;
               printf("See log file for details...\n");
             }
             fprintf(ficlog,"Age %d", i);
           }
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
           }
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
               if(first==1){
                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
               if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
           }
   
           for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
           }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
             posprop += prop[jk][i];
           }
           for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
               if(first==1)
                 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);
             }else{
               if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
             if( i <= iagemax){
               if(pos>=1.e-5){
                 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]);*/
               }
               else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
           }
           
           for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
               if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
           if(i <= iagemax)
             fprintf(ficresp,"\n");
           if(first==1)
             printf("Others in log...\n");
           fprintf(ficlog,"\n");
         }
         /*}*/
     }
     dateintmean=dateintsum/k2cpt; 
    
     fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
   }
   
   /************ Prevalence ********************/
   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
     /* 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).
        We still use firstpass and lastpass as another selection.
     */
    
     int i, m, jk, j1, bool, z1,j;
   
     double **prop;
     double posprop; 
     double  y2; /* in fractional years */
     int iagemin, iagemax;
     int first; /** to stop verbosity which is redirected to log file */
   
     iagemin= (int) agemin;
     iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
     
     /*j=cptcoveff;*/
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
     first=1;
     for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
       /*for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;*/
         
         for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
        
         for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
           if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
           } 
           if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
               }
             } /* end selection of waves */
           }
         }
         for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
           } 
           
           for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
               } else{
                 if(first==1){
                   first=0;
                   printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                 }
               }
             } 
           }/* end jk */ 
         }/* end i */ 
       /*} *//* end i1 */
     } /* end j1 */
     
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   
   /************* Waves Concatenation ***************/
   
   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)
   {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or 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.
        */
   
     int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
     int first;
     int j, k=0,jk, ju, jl;
     double sum=0.;
     first=0;
     jmin=100000;
     jmax=-1;
     jmean=0.;
     for(i=1; i<=imx; i++){
       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;
         if(m >=lastpass)
           break;
         else
           m++;
       }/* end while */
       if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
         mw[mi][i]=m;
       }
   
       wav[i]=mi;
       if(mi==0){
         nbwarn++;
         if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
         }
         if(first==1){
           fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
       } /* end mi==0 */
     } /* End individuals */
   
     for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
           dh[mi][i]=1;
         else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
                 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]);
                 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);
               }
               k=k+1;
               if (j >= jmax){
                 jmax=j;
                 ijmax=i;
               }
               if (j <= jmin){
                 jmin=j;
                 ijmin=i;
               }
               sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
           }
           else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        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]); */
   
             k=k+1;
             if (j >= jmax) {
               jmax=j;
               ijmax=i;
             }
             else if (j <= jmin){
               jmin=j;
               ijmin=i;
             }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
               nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               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]);
             }
             sum=sum+j;
           }
           jk= j/stepm;
           jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
               dh[mi][i]=jk;
               bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
           }else{
             if(jl <= -ju){
               dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
                                    */
             }
             else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
             if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
           } /* end if mle */
         }
       } /* end wave */
     }
     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);
    }
   
   /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
     /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
      * Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
      * nbcode[Tvar[j]][1]= 
     */
   
     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int modmaxcovj=0; /* Modality max of covariates j */
     int cptcode=0; /* Modality max of covariates j */
     int modmincovj=0; /* Modality min of covariates j */
   
   
     cptcoveff=0; 
    
     for (k=-1; k < maxncov; k++) Ndum[k]=0;
     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
     /* Loop on covariates without age and products */
     for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
       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*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                       * If product of Vn*Vm, still boolean *:
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                       * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
           modmaxcovj=ij; 
         else if (ij < modmincovj) 
           modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
           exit(1);
         }else
         Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         /* getting the maximum value of the modality of the covariate
            (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
            female is 1, then modmaxcovj=1.*/
       } /* end for loop on individuals */
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       cptcode=modmaxcovj;
       /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
      /*for (i=0; i<=cptcode; i++) {*/
       for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
         if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         }
         /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
            historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       } /* Ndum[-1] number of undefined modalities */
   
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
          If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
          modmincovj=3; modmaxcovj = 7;
          There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
          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.
          nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
          nbcode[Tvar[j]][3]=2;
       */
       ij=1; /* ij is similar to i but can jumps over null modalities */
       for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           /*recode from 0 */
           if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             nbcode[Tvar[j]][ij]=k;  /* stores the modality k in an array nbcode. 
                                        k is a modality. If we have model=V1+V1*sex 
                                        then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             ij++;
           }
           if (ij > ncodemax[j]) break; 
         }  /* end of loop on */
       } /* 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*/  
     
    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     
     for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      Ndum[ij]++; /* Might be supersed V1 + V1*age */
    } 
   
    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) */
      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      if((Ndum[i]!=0) && (i<=ncovcol)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
        ij++;
      }else
          Tvaraff[ij]=0;
    }
    ij--;
    cptcoveff=ij; /*Number of total covariates*/
   
   }
   
   
   /*********** 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[] )
   
   {
     /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3mat;
     double eip;
   
     pstamp(ficreseij);
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       }
       fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficreseij,"\n");
   
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     agelim=AGESUP;
     /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   
   {
     /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           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.1.7  
changed lines
  Added in v.1.189


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