Diff for /imach/src/imach.c between versions 1.17 and 1.181

version 1.17, 2002/02/20 17:15:02 version 1.181, 2015/02/11 23:22:24
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 1.181  2015/02/11 23:22:24  brouard
   individuals from different ages are interviewed on their health status    Summary: Comments on Powell added
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Author:
   Health expectancies are computed from the transistions observed between  
   waves and are computed for each degree of severity of disability (number    Revision 1.180  2015/02/11 17:33:45  brouard
   of life states). More degrees you consider, more time is necessary to    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.179  2015/01/04 09:57:06  brouard
   the probabibility to be observed in state j at the second wave conditional    Summary: back to OS/X
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Revision 1.178  2015/01/04 09:35:48  brouard
   is a covariate. If you want to have a more complex model than "constant and    *** empty log message ***
   age", you should modify the program where the markup  
     *Covariates have to be included here again* invites you to do it.    Revision 1.177  2015/01/03 18:40:56  brouard
   More covariates you add, less is the speed of the convergence.    Summary: Still testing ilc32 on OSX
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.176  2015/01/03 16:45:04  brouard
   delay between waves is not identical for each individual, or if some    *** empty log message ***
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.175  2015/01/03 16:33:42  brouard
   hPijx is the probability to be    *** empty log message ***
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.174  2015/01/03 16:15:49  brouard
   unobserved intermediate  states. This elementary transition (by month or    Summary: Still in cross-compilation
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.173  2015/01/03 12:06:26  brouard
   and the contribution of each individual to the likelihood is simply hPijx.    Summary: trying to detect cross-compilation
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.172  2014/12/27 12:07:47  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.171  2014/12/23 13:26:59  brouard
            Institut national d'études démographiques, Paris.    Summary: Back from Visual C
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Still problem with utsname.h on Windows
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.170  2014/12/23 11:17:12  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Summary: Cleaning some \%% back to %%
   **********************************************************************/  
      The escape was mandatory for a specific compiler (which one?), but too many warnings.
 #include <math.h>  
 #include <stdio.h>    Revision 1.169  2014/12/22 23:08:31  brouard
 #include <stdlib.h>    Summary: 0.98p
 #include <unistd.h>  
     Outputs some informations on compiler used, OS etc. Testing on different platforms.
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    Revision 1.168  2014/12/22 15:17:42  brouard
 /*#define DEBUG*/    Summary: update
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.167  2014/12/22 13:50:56  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Summary: Testing uname and compiler version and if compiled 32 or 64
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Testing on Linux 64
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.166  2014/12/22 11:40:47  brouard
 #define NINTERVMAX 8    *** empty log message ***
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.165  2014/12/16 11:20:36  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: After compiling on Visual C
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    * imach.c (Module): Merging 1.61 to 1.162
 #define AGESUP 130  
 #define AGEBASE 40    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
   
 int nvar;    * imach.c (Module): Merging 1.61 to 1.162
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.163  2014/12/16 10:30:11  brouard
 int nlstate=2; /* Number of live states */    * imach.c (Module): Merging 1.61 to 1.162
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.162  2014/09/25 11:43:39  brouard
 int popbased=0;    Summary: temporary backup 0.99!
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.1  2014/09/16 11:06:58  brouard
 int maxwav; /* Maxim number of waves */    Summary: With some code (wrong) for nlopt
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Author:
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.161  2014/09/15 20:41:41  brouard
 double jmean; /* Mean space between 2 waves */    Summary: Problem with macro SQR on Intel compiler
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.160  2014/09/02 09:24:05  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    *** empty log message ***
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.159  2014/09/01 10:34:10  brouard
   char filerese[FILENAMELENGTH];    Summary: WIN32
  FILE  *ficresvij;    Author: Brouard
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.158  2014/08/27 17:11:51  brouard
   char fileresvpl[FILENAMELENGTH];    *** empty log message ***
   
 #define NR_END 1    Revision 1.157  2014/08/27 16:26:55  brouard
 #define FREE_ARG char*    Summary: Preparing windows Visual studio version
 #define FTOL 1.0e-10    Author: Brouard
   
 #define NRANSI    In order to compile on Visual studio, time.h is now correct and time_t
 #define ITMAX 200    and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
 #define TOL 2.0e-4    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.156  2014/08/25 20:10:10  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    *** empty log message ***
   
 #define GOLD 1.618034    Revision 1.155  2014/08/25 18:32:34  brouard
 #define GLIMIT 100.0    Summary: New compile, minor changes
 #define TINY 1.0e-20    Author: Brouard
   
 static double maxarg1,maxarg2;    Revision 1.154  2014/06/20 17:32:08  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Summary: Outputs now all graphs of convergence to period prevalence
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.153  2014/06/20 16:45:46  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Summary: If 3 live state, convergence to period prevalence on same graph
 #define rint(a) floor(a+0.5)    Author: Brouard
   
 static double sqrarg;    Revision 1.152  2014/06/18 17:54:09  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.151  2014/06/18 16:43:30  brouard
 int imx;    *** empty log message ***
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.150  2014/06/18 16:42:35  brouard
     Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 int m,nb;    Author: brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.149  2014/06/18 15:51:14  brouard
 double **pmmij, ***probs, ***mobaverage;    Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
 double *weight;  
 int **s; /* Status */    Revision 1.148  2014/06/17 17:38:48  brouard
 double *agedc, **covar, idx;    Summary: Nothing new
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Author: Brouard
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Just a new packaging for OS/X version 0.98nS
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.147  2014/06/16 10:33:11  brouard
 /**************** split *************************/    *** empty log message ***
 static  int split( char *path, char *dirc, char *name )  
 {    Revision 1.146  2014/06/16 10:20:28  brouard
    char *s;                             /* pointer */    Summary: Merge
    int  l1, l2;                         /* length counters */    Author: Brouard
   
    l1 = strlen( path );                 /* length of path */    Merge, before building revised version.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.145  2014/06/10 21:23:15  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    Summary: Debugging with valgrind
 #if     defined(__bsd__)                /* get current working directory */    Author: Nicolas Brouard
       extern char       *getwd( );  
     Lot of changes in order to output the results with some covariates
       if ( getwd( dirc ) == NULL ) {    After the Edimburgh REVES conference 2014, it seems mandatory to
 #else    improve the code.
       extern char       *getcwd( );    No more memory valgrind error but a lot has to be done in order to
     continue the work of splitting the code into subroutines.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Also, decodemodel has been improved. Tricode is still not
 #endif    optimal. nbcode should be improved. Documentation has been added in
          return( GLOCK_ERROR_GETCWD );    the source code.
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.143  2014/01/26 09:45:38  brouard
    } else {                             /* strip direcotry from path */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.142  2014/01/26 03:57:36  brouard
       dirc[l1-l2] = 0;                  /* add zero */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    }  
    l1 = strlen( dirc );                 /* length of directory */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
    return( 0 );                         /* we're done */    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...
   
     Revision 1.140  2011/09/02 10:37:54  brouard
 /******************************************/    Summary: times.h is ok with mingw32 now.
   
 void replace(char *s, char*t)    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.
   int i;    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   int lg=20;  
   i=0;    Revision 1.138  2010/04/30 18:19:40  brouard
   lg=strlen(t);    *** empty log message ***
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.137  2010/04/29 18:11:38  brouard
     if (t[i]== '\\') s[i]='/';    (Module): Checking covariates for more complex models
   }    than V1+V2. A lot of change to be done. Unstable.
 }  
     Revision 1.136  2010/04/26 20:30:53  brouard
 int nbocc(char *s, char occ)    (Module): merging some libgsl code. Fixing computation
 {    of likelione (using inter/intrapolation if mle = 0) in order to
   int i,j=0;    get same likelihood as if mle=1.
   int lg=20;    Some cleaning of code and comments added.
   i=0;  
   lg=strlen(s);    Revision 1.135  2009/10/29 15:33:14  brouard
   for(i=0; i<= lg; i++) {    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   if  (s[i] == occ ) j++;  
   }    Revision 1.134  2009/10/29 13:18:53  brouard
   return j;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 }  
     Revision 1.133  2009/07/06 10:21:25  brouard
 void cutv(char *u,char *v, char*t, char occ)    just nforces
 {  
   int i,lg,j,p=0;    Revision 1.132  2009/07/06 08:22:05  brouard
   i=0;    Many tings
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.131  2009/06/20 16:22:47  brouard
   }    Some dimensions resccaled
   
   lg=strlen(t);    Revision 1.130  2009/05/26 06:44:34  brouard
   for(j=0; j<p; j++) {    (Module): Max Covariate is now set to 20 instead of 8. A
     (u[j] = t[j]);    lot of cleaning with variables initialized to 0. Trying to make
   }    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
      u[p]='\0';  
     Revision 1.129  2007/08/31 13:49:27  lievre
    for(j=0; j<= lg; j++) {    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.128  2006/06/30 13:02:05  brouard
 }    (Module): Clarifications on computing e.j
   
 /********************** nrerror ********************/    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 void nrerror(char error_text[])    imach-114 because nhstepm was no more computed in the age
 {    loop. Now we define nhstepma in the age loop.
   fprintf(stderr,"ERREUR ...\n");    (Module): In order to speed up (in case of numerous covariates) we
   fprintf(stderr,"%s\n",error_text);    compute health expectancies (without variances) in a first step
   exit(1);    and then all the health expectancies with variances or standard
 }    deviation (needs data from the Hessian matrices) which slows the
 /*********************** vector *******************/    computation.
 double *vector(int nl, int nh)    In the future we should be able to stop the program is only health
 {    expectancies and graph are needed without standard deviations.
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.126  2006/04/28 17:23:28  brouard
   if (!v) nrerror("allocation failure in vector");    (Module): Yes the sum of survivors was wrong since
   return v-nl+NR_END;    imach-114 because nhstepm was no more computed in the age
 }    loop. Now we define nhstepma in the age loop.
     Version 0.98h
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.125  2006/04/04 15:20:31  lievre
 {    Errors in calculation of health expectancies. Age was not initialized.
   free((FREE_ARG)(v+nl-NR_END));    Forecasting file added.
 }  
     Revision 1.124  2006/03/22 17:13:53  lievre
 /************************ivector *******************************/    Parameters are printed with %lf instead of %f (more numbers after the comma).
 int *ivector(long nl,long nh)    The log-likelihood is printed in the log file
 {  
   int *v;    Revision 1.123  2006/03/20 10:52:43  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    * imach.c (Module): <title> changed, corresponds to .htm file
   if (!v) nrerror("allocation failure in ivector");    name. <head> headers where missing.
   return v-nl+NR_END;  
 }    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 /******************free ivector **************************/    otherwise the weight is truncated).
 void free_ivector(int *v, long nl, long nh)    Modification of warning when the covariates values are not 0 or
 {    1.
   free((FREE_ARG)(v+nl-NR_END));    Version 0.98g
 }  
     Revision 1.122  2006/03/20 09:45:41  brouard
 /******************* imatrix *******************************/    (Module): Weights can have a decimal point as for
 int **imatrix(long nrl, long nrh, long ncl, long nch)    English (a comma might work with a correct LC_NUMERIC environment,
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    otherwise the weight is truncated).
 {    Modification of warning when the covariates values are not 0 or
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    1.
   int **m;    Version 0.98g
    
   /* allocate pointers to rows */    Revision 1.121  2006/03/16 17:45:01  lievre
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    * imach.c (Module): Comments concerning covariates added
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    * imach.c (Module): refinements in the computation of lli if
   m -= nrl;    status=-2 in order to have more reliable computation if stepm is
      not 1 month. Version 0.98f
    
   /* allocate rows and set pointers to them */    Revision 1.120  2006/03/16 15:10:38  lievre
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    (Module): refinements in the computation of lli if
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    status=-2 in order to have more reliable computation if stepm is
   m[nrl] += NR_END;    not 1 month. Version 0.98f
   m[nrl] -= ncl;  
      Revision 1.119  2006/03/15 17:42:26  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): Bug if status = -2, the loglikelihood was
      computed as likelihood omitting the logarithm. Version O.98e
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.118  2006/03/14 18:20:07  brouard
 }    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 /****************** free_imatrix *************************/    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): Function pstamp added
       int **m;    (Module): Version 0.98d
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.117  2006/03/14 17:16:22  brouard
 {    (Module): varevsij Comments added explaining the second
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    table of variances if popbased=1 .
   free((FREE_ARG) (m+nrl-NR_END));    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 }    (Module): Function pstamp added
     (Module): Version 0.98d
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.116  2006/03/06 10:29:27  brouard
 {    (Module): Variance-covariance wrong links and
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    varian-covariance of ej. is needed (Saito).
   double **m;  
     Revision 1.115  2006/02/27 12:17:45  brouard
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Module): One freematrix added in mlikeli! 0.98c
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.114  2006/02/26 12:57:58  brouard
   m -= nrl;    (Module): Some improvements in processing parameter
     filename with strsep.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.113  2006/02/24 14:20:24  brouard
   m[nrl] += NR_END;    (Module): Memory leaks checks with valgrind and:
   m[nrl] -= ncl;    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.112  2006/01/30 09:55:26  brouard
 }    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 /*************************free matrix ************************/    Revision 1.111  2006/01/25 20:38:18  brouard
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    (Module): Lots of cleaning and bugs added (Gompertz)
 {    (Module): Comments can be added in data file. Missing date values
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    can be a simple dot '.'.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Revision 1.109  2006/01/24 19:37:15  brouard
 {    (Module): Comments (lines starting with a #) are allowed in data.
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    To be fixed
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.107  2006/01/19 16:20:37  brouard
   m -= nrl;    Test existence of gnuplot in imach path
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.106  2006/01/19 13:24:36  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Some cleaning and links added in html output
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Revision 1.104  2005/09/30 16:11:43  lievre
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    (Module): sump fixed, loop imx fixed, and simplifications.
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    (Module): If the status is missing at the last wave but we know
   m[nrl][ncl] += NR_END;    that the person is alive, then we can code his/her status as -2
   m[nrl][ncl] -= nll;    (instead of missing=-1 in earlier versions) and his/her
   for (j=ncl+1; j<=nch; j++)    contributions to the likelihood is 1 - Prob of dying from last
     m[nrl][j]=m[nrl][j-1]+nlay;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
      the healthy state at last known wave). Version is 0.98
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Revision 1.103  2005/09/30 15:54:49  lievre
     for (j=ncl+1; j<=nch; j++)    (Module): sump fixed, loop imx fixed, and simplifications.
       m[i][j]=m[i][j-1]+nlay;  
   }    Revision 1.102  2004/09/15 17:31:30  brouard
   return m;    Add the possibility to read data file including tab characters.
 }  
     Revision 1.101  2004/09/15 10:38:38  brouard
 /*************************free ma3x ************************/    Fix on curr_time
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    Revision 1.100  2004/07/12 18:29:06  brouard
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Add version for Mac OS X. Just define UNIX in Makefile
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.99  2004/06/05 08:57:40  brouard
 }    *** empty log message ***
   
 /***************** f1dim *************************/    Revision 1.98  2004/05/16 15:05:56  brouard
 extern int ncom;    New version 0.97 . First attempt to estimate force of mortality
 extern double *pcom,*xicom;    directly from the data i.e. without the need of knowing the health
 extern double (*nrfunc)(double []);    state at each age, but using a Gompertz model: log u =a + b*age .
      This is the basic analysis of mortality and should be done before any
 double f1dim(double x)    other analysis, in order to test if the mortality estimated from the
 {    cross-longitudinal survey is different from the mortality estimated
   int j;    from other sources like vital statistic data.
   double f;  
   double *xt;    The same imach parameter file can be used but the option for mle should be -3.
    
   xt=vector(1,ncom);    Agnès, who wrote this part of the code, tried to keep most of the
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    former routines in order to include the new code within the former code.
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    The output is very simple: only an estimate of the intercept and of
   return f;    the slope with 95% confident intervals.
 }  
     Current limitations:
 /*****************brent *************************/    A) Even if you enter covariates, i.e. with the
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 {    B) There is no computation of Life Expectancy nor Life Table.
   int iter;  
   double a,b,d,etemp;    Revision 1.97  2004/02/20 13:25:42  lievre
   double fu,fv,fw,fx;    Version 0.96d. Population forecasting command line is (temporarily)
   double ftemp;    suppressed.
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    Revision 1.96  2003/07/15 15:38:55  brouard
      * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   a=(ax < cx ? ax : cx);    rewritten within the same printf. Workaround: many printfs.
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.95  2003/07/08 07:54:34  brouard
   fw=fv=fx=(*f)(x);    * imach.c (Repository):
   for (iter=1;iter<=ITMAX;iter++) {    (Repository): Using imachwizard code to output a more meaningful covariance
     xm=0.5*(a+b);    matrix (cov(a12,c31) instead of numbers.
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    Revision 1.94  2003/06/27 13:00:02  brouard
     printf(".");fflush(stdout);    Just cleaning
 #ifdef DEBUG  
     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);    Revision 1.93  2003/06/25 16:33:55  brouard
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    (Module): On windows (cygwin) function asctime_r doesn't
 #endif    exist so I changed back to asctime which exists.
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    (Module): Version 0.96b
       *xmin=x;  
       return fx;    Revision 1.92  2003/06/25 16:30:45  brouard
     }    (Module): On windows (cygwin) function asctime_r doesn't
     ftemp=fu;    exist so I changed back to asctime which exists.
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    Revision 1.91  2003/06/25 15:30:29  brouard
       q=(x-v)*(fx-fw);    * imach.c (Repository): Duplicated warning errors corrected.
       p=(x-v)*q-(x-w)*r;    (Repository): Elapsed time after each iteration is now output. It
       q=2.0*(q-r);    helps to forecast when convergence will be reached. Elapsed time
       if (q > 0.0) p = -p;    is stamped in powell.  We created a new html file for the graphs
       q=fabs(q);    concerning matrix of covariance. It has extension -cov.htm.
       etemp=e;  
       e=d;    Revision 1.90  2003/06/24 12:34:15  brouard
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    (Module): Some bugs corrected for windows. Also, when
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    mle=-1 a template is output in file "or"mypar.txt with the design
       else {    of the covariance matrix to be input.
         d=p/q;  
         u=x+d;    Revision 1.89  2003/06/24 12:30:52  brouard
         if (u-a < tol2 || b-u < tol2)    (Module): Some bugs corrected for windows. Also, when
           d=SIGN(tol1,xm-x);    mle=-1 a template is output in file "or"mypar.txt with the design
       }    of the covariance matrix to be input.
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    Revision 1.88  2003/06/23 17:54:56  brouard
     }    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    Revision 1.87  2003/06/18 12:26:01  brouard
     if (fu <= fx) {    Version 0.96
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)    Revision 1.86  2003/06/17 20:04:08  brouard
         SHFT(fv,fw,fx,fu)    (Module): Change position of html and gnuplot routines and added
         } else {    routine fileappend.
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {    Revision 1.85  2003/06/17 13:12:43  brouard
             v=w;    * imach.c (Repository): Check when date of death was earlier that
             w=u;    current date of interview. It may happen when the death was just
             fv=fw;    prior to the death. In this case, dh was negative and likelihood
             fw=fu;    was wrong (infinity). We still send an "Error" but patch by
           } else if (fu <= fv || v == x || v == w) {    assuming that the date of death was just one stepm after the
             v=u;    interview.
             fv=fu;    (Repository): Because some people have very long ID (first column)
           }    we changed int to long in num[] and we added a new lvector for
         }    memory allocation. But we also truncated to 8 characters (left
   }    truncation)
   nrerror("Too many iterations in brent");    (Repository): No more line truncation errors.
   *xmin=x;  
   return fx;    Revision 1.84  2003/06/13 21:44:43  brouard
 }    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 /****************** mnbrak ***********************/    many times. Probs is memory consuming and must be used with
     parcimony.
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
             double (*func)(double))  
 {    Revision 1.83  2003/06/10 13:39:11  lievre
   double ulim,u,r,q, dum;    *** empty log message ***
   double fu;  
      Revision 1.82  2003/06/05 15:57:20  brouard
   *fa=(*func)(*ax);    Add log in  imach.c and  fullversion number is now printed.
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  */
     SHFT(dum,*ax,*bx,dum)  /*
       SHFT(dum,*fb,*fa,dum)     Interpolated Markov Chain
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);    Short summary of the programme:
   *fc=(*func)(*cx);    
   while (*fb > *fc) {    This program computes Healthy Life Expectancies from
     r=(*bx-*ax)*(*fb-*fc);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     q=(*bx-*cx)*(*fb-*fa);    first survey ("cross") where individuals from different ages are
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    interviewed on their health status or degree of disability (in the
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    case of a health survey which is our main interest) -2- at least a
     ulim=(*bx)+GLIMIT*(*cx-*bx);    second wave of interviews ("longitudinal") which measure each change
     if ((*bx-u)*(u-*cx) > 0.0) {    (if any) in individual health status.  Health expectancies are
       fu=(*func)(u);    computed from the time spent in each health state according to a
     } else if ((*cx-u)*(u-ulim) > 0.0) {    model. More health states you consider, more time is necessary to reach the
       fu=(*func)(u);    Maximum Likelihood of the parameters involved in the model.  The
       if (fu < *fc) {    simplest model is the multinomial logistic model where pij is the
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    probability to be observed in state j at the second wave
           SHFT(*fb,*fc,fu,(*func)(u))    conditional to be observed in state i at the first wave. Therefore
           }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    'age' is age and 'sex' is a covariate. If you want to have a more
       u=ulim;    complex model than "constant and age", you should modify the program
       fu=(*func)(u);    where the markup *Covariates have to be included here again* invites
     } else {    you to do it.  More covariates you add, slower the
       u=(*cx)+GOLD*(*cx-*bx);    convergence.
       fu=(*func)(u);  
     }    The advantage of this computer programme, compared to a simple
     SHFT(*ax,*bx,*cx,u)    multinomial logistic model, is clear when the delay between waves is not
       SHFT(*fa,*fb,*fc,fu)    identical for each individual. Also, if a individual missed an
       }    intermediate interview, the information is lost, but taken into
 }    account using an interpolation or extrapolation.  
   
 /*************** linmin ************************/    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
 int ncom;    split into an exact number (nh*stepm) of unobserved intermediate
 double *pcom,*xicom;    states. This elementary transition (by month, quarter,
 double (*nrfunc)(double []);    semester or year) is modelled as a multinomial logistic.  The hPx
      matrix is simply the matrix product of nh*stepm elementary matrices
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    and the contribution of each individual to the likelihood is simply
 {    hPijx.
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);    Also this programme outputs the covariance matrix of the parameters but also
   double f1dim(double x);    of the life expectancies. It also computes the period (stable) prevalence. 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    
               double *fc, double (*func)(double));    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   int j;             Institut national d'études démographiques, Paris.
   double xx,xmin,bx,ax;    This software have been partly granted by Euro-REVES, a concerted action
   double fx,fb,fa;    from the European Union.
      It is copyrighted identically to a GNU software product, ie programme and
   ncom=n;    software can be distributed freely for non commercial use. Latest version
   pcom=vector(1,n);    can be accessed at http://euroreves.ined.fr/imach .
   xicom=vector(1,n);  
   nrfunc=func;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   for (j=1;j<=n;j++) {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     pcom[j]=p[j];    
     xicom[j]=xi[j];    **********************************************************************/
   }  /*
   ax=0.0;    main
   xx=1.0;    read parameterfile
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    read datafile
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    concatwav
 #ifdef DEBUG    freqsummary
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    if (mle >= 1)
 #endif      mlikeli
   for (j=1;j<=n;j++) {    print results files
     xi[j] *= xmin;    if mle==1 
     p[j] += xi[j];       computes hessian
   }    read end of parameter file: agemin, agemax, bage, fage, estepm
   free_vector(xicom,1,n);        begin-prev-date,...
   free_vector(pcom,1,n);    open gnuplot file
 }    open html file
     period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 /*************** powell ************************/     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
             double (*func)(double []))      freexexit2 possible for memory heap.
 {  
   void linmin(double p[], double xi[], int n, double *fret,    h Pij x                         | pij_nom  ficrestpij
               double (*func)(double []));     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   int i,ibig,j;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   double del,t,*pt,*ptt,*xit;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   double fp,fptt;  
   double *xits;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   pt=vector(1,n);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   ptt=vector(1,n);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   xit=vector(1,n);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   xits=vector(1,n);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];    forecasting if prevfcast==1 prevforecast call prevalence()
   for (*iter=1;;++(*iter)) {    health expectancies
     fp=(*fret);    Variance-covariance of DFLE
     ibig=0;    prevalence()
     del=0.0;     movingaverage()
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    varevsij() 
     for (i=1;i<=n;i++)    if popbased==1 varevsij(,popbased)
       printf(" %d %.12f",i, p[i]);    total life expectancies
     printf("\n");    Variance of period (stable) prevalence
     for (i=1;i<=n;i++) {   end
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  */
       fptt=(*fret);  
 #ifdef DEBUG  #define POWELL /* Instead of NLOPT */
       printf("fret=%lf \n",*fret);  #define POWELLDIRECT /* Directest to decide new direction instead of Powell test */
 #endif  
       printf("%d",i);fflush(stdout);  #include <math.h>
       linmin(p,xit,n,fret,func);  #include <stdio.h>
       if (fabs(fptt-(*fret)) > del) {  #include <stdlib.h>
         del=fabs(fptt-(*fret));  #include <string.h>
         ibig=i;  
       }  #ifdef _WIN32
 #ifdef DEBUG  #include <io.h>
       printf("%d %.12e",i,(*fret));  #include <windows.h>
       for (j=1;j<=n;j++) {  #include <tchar.h>
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #else
         printf(" x(%d)=%.12e",j,xit[j]);  #include <unistd.h>
       }  #endif
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  #include <limits.h>
       printf("\n");  #include <sys/types.h>
 #endif  
     }  #if defined(__GNUC__)
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #include <sys/utsname.h> /* Doesn't work on Windows */
 #ifdef DEBUG  #endif
       int k[2],l;  
       k[0]=1;  #include <sys/stat.h>
       k[1]=-1;  #include <errno.h>
       printf("Max: %.12e",(*func)(p));  /* extern int errno; */
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /* #ifdef LINUX */
       printf("\n");  /* #include <time.h> */
       for(l=0;l<=1;l++) {  /* #include "timeval.h" */
         for (j=1;j<=n;j++) {  /* #else */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /* #include <sys/time.h> */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  /* #endif */
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #include <time.h>
       }  
 #endif  #ifdef GSL
   #include <gsl/gsl_errno.h>
   #include <gsl/gsl_multimin.h>
       free_vector(xit,1,n);  #endif
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  #ifdef NLOPT
       return;  #include <nlopt.h>
     }  typedef struct {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    double (* function)(double [] );
     for (j=1;j<=n;j++) {  } myfunc_data ;
       ptt[j]=2.0*p[j]-pt[j];  #endif
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  /* #include <libintl.h> */
     }  /* #define _(String) gettext (String) */
     fptt=(*func)(ptt);  
     if (fptt < fp) {  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  #define GNUPLOTPROGRAM "gnuplot"
         linmin(p,xit,n,fret,func);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         for (j=1;j<=n;j++) {  #define FILENAMELENGTH 132
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
         }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         for(j=1;j<=n;j++)  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
           printf(" %.12e",xit[j]);  
         printf("\n");  #define NINTERVMAX 8
 #endif  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       }  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     }  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   }  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
 }  #define MAXN 20000
   #define YEARM 12. /**< Number of months per year */
 /**** Prevalence limit ****************/  #define AGESUP 130
   #define AGEBASE 40
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 {  #ifdef _WIN32
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #define DIRSEPARATOR '\\'
      matrix by transitions matrix until convergence is reached */  #define CHARSEPARATOR "\\"
   #define ODIRSEPARATOR '/'
   int i, ii,j,k;  #else
   double min, max, maxmin, maxmax,sumnew=0.;  #define DIRSEPARATOR '/'
   double **matprod2();  #define CHARSEPARATOR "/"
   double **out, cov[NCOVMAX], **pmij();  #define ODIRSEPARATOR '\\'
   double **newm;  #endif
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   /* $Id$ */
   for (ii=1;ii<=nlstate+ndeath;ii++)  /* $State$ */
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char version[]="Imach version 0.98p, Février 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
     }  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
    cov[1]=1.;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
    int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int nvar=0, nforce=0; /* Number of variables, number of forces */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
     newm=savm;  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     /* Covariates have to be included here again */  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
      cov[2]=agefin;  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
    int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       for (k=1; k<=cptcovn;k++) {  int cptcovprodnoage=0; /**< Number of covariate products without age */   
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int cptcoveff=0; /* Total number of covariates to vary for printing results */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  int cptcov=0; /* Working variable */
       }  int npar=NPARMAX;
       for (k=1; k<=cptcovage;k++)  int nlstate=2; /* Number of live states */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int ndeath=1; /* Number of dead states */
       for (k=1; k<=cptcovprod;k++)  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  int popbased=0;
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int *wav; /* Number of waves for this individuual 0 is possible */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  int maxwav=0; /* Maxim number of waves */
   int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     savm=oldm;                     to the likelihood and the sum of weights (done by funcone)*/
     oldm=newm;  int mle=1, weightopt=0;
     maxmax=0.;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     for(j=1;j<=nlstate;j++){  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       min=1.;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       max=0.;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       for(i=1; i<=nlstate; i++) {  int countcallfunc=0;  /* Count the number of calls to func */
         sumnew=0;  double jmean=1; /* Mean space between 2 waves */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double **matprod2(); /* test */
         prlim[i][j]= newm[i][j]/(1-sumnew);  double **oldm, **newm, **savm; /* Working pointers to matrices */
         max=FMAX(max,prlim[i][j]);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
         min=FMIN(min,prlim[i][j]);  /*FILE *fic ; */ /* Used in readdata only */
       }  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       maxmin=max-min;  FILE *ficlog, *ficrespow;
       maxmax=FMAX(maxmax,maxmin);  int globpr=0; /* Global variable for printing or not */
     }  double fretone; /* Only one call to likelihood */
     if(maxmax < ftolpl){  long ipmx=0; /* Number of contributions */
       return prlim;  double sw; /* Sum of weights */
     }  char filerespow[FILENAMELENGTH];
   }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 }  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 /*************** transition probabilities ***************/  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   double s1, s2;  FILE *ficresstdeij;
   /*double t34;*/  char fileresstde[FILENAMELENGTH];
   int i,j,j1, nc, ii, jj;  FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
     for(i=1; i<= nlstate; i++){  FILE  *ficresvij;
     for(j=1; j<i;j++){  char fileresv[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  FILE  *ficresvpl;
         /*s2 += param[i][j][nc]*cov[nc];*/  char fileresvpl[FILENAMELENGTH];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char title[MAXLINE];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       ps[i][j]=s2;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char command[FILENAMELENGTH];
     }  int  outcmd=0;
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
       ps[i][j]=(s2);  char fileregp[FILENAMELENGTH];
     }  char popfile[FILENAMELENGTH];
   }  
     /*ps[3][2]=1;*/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
   for(i=1; i<= nlstate; i++){  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
      s1=0;  /* struct timezone tzp; */
     for(j=1; j<i; j++)  /* extern int gettimeofday(); */
       s1+=exp(ps[i][j]);  struct tm tml, *gmtime(), *localtime();
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  extern time_t time();
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     for(j=i+1; j<=nlstate+ndeath; j++)  struct tm tm;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  char strcurr[80], strfor[80];
   } /* end i */  
   char *endptr;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  long lval;
     for(jj=1; jj<= nlstate+ndeath; jj++){  double dval;
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  #define NR_END 1
     }  #define FREE_ARG char*
   }  #define FTOL 1.0e-10
   
   #define NRANSI 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #define ITMAX 200 
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  #define TOL 2.0e-4 
    }  
     printf("\n ");  #define CGOLD 0.3819660 
     }  #define ZEPS 1.0e-10 
     printf("\n ");printf("%lf ",cov[2]);*/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  #define GOLD 1.618034 
   goto end;*/  #define GLIMIT 100.0 
     return ps;  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 /**************** Product of 2 matrices ******************/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  #define rint(a) floor(a+0.5)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
   /* in, b, out are matrice of pointers which should have been initialized  /* #define mytinydouble 1.0e-16 */
      before: only the contents of out is modified. The function returns  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
      a pointer to pointers identical to out */  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   long i, j, k;  /* static double dsqrarg; */
   for(i=nrl; i<= nrh; i++)  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
     for(k=ncolol; k<=ncoloh; k++)  static double sqrarg;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         out[i][k] +=in[i][j]*b[j][k];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
   return out;  
 }  int imx; 
   int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
 /************* Higher Matrix Product ***************/  
   int estepm;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  int m,nb;
      duration (i.e. until  long *num;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
      (typically every 2 years instead of every month which is too big).  double **pmmij, ***probs;
      Model is determined by parameters x and covariates have to be  double *ageexmed,*agecens;
      included manually here.  double dateintmean=0;
   
      */  double *weight;
   int **s; /* Status */
   int i, j, d, h, k;  double *agedc;
   double **out, cov[NCOVMAX];  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   double **newm;                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   /* Hstepm could be zero and should return the unit matrix */  double  idx; 
   for (i=1;i<=nlstate+ndeath;i++)  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
     for (j=1;j<=nlstate+ndeath;j++){  int *Ndum; /** Freq of modality (tricode */
       oldm[i][j]=(i==j ? 1.0 : 0.0);  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     }  double *lsurv, *lpop, *tpop;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
     for(d=1; d <=hstepm; d++){  double ftolhess; /**< Tolerance for computing hessian */
       newm=savm;  
       /* Covariates have to be included here again */  /**************** split *************************/
       cov[1]=1.;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       for (k=1; k<=cptcovage;k++)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    */ 
       for (k=1; k<=cptcovprod;k++)    char  *ss;                            /* pointer */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    int   l1, l2;                         /* length counters */
   
     l1 = strlen(path );                   /* length of path */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    if ( ss == NULL ) {                   /* no directory, so determine current directory */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      strcpy( name, path );               /* we got the fullname name because no directory */
       savm=oldm;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       oldm=newm;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     }      /* get current working directory */
     for(i=1; i<=nlstate+ndeath; i++)      /*    extern  char* getcwd ( char *buf , int len);*/
       for(j=1;j<=nlstate+ndeath;j++) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         po[i][j][h]=newm[i][j];        return( GLOCK_ERROR_GETCWD );
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      }
          */      /* got dirc from getcwd*/
       }      printf(" DIRC = %s \n",dirc);
   } /* end h */    } else {                              /* strip direcotry from path */
   return po;      ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 /*************** log-likelihood *************/      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 double func( double *x)      dirc[l1-l2] = 0;                    /* add zero */
 {      printf(" DIRC2 = %s \n",dirc);
   int i, ii, j, k, mi, d, kk;    }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    /* We add a separator at the end of dirc if not exists */
   double **out;    l1 = strlen( dirc );                  /* length of directory */
   double sw; /* Sum of weights */    if( dirc[l1-1] != DIRSEPARATOR ){
   double lli; /* Individual log likelihood */      dirc[l1] =  DIRSEPARATOR;
   long ipmx;      dirc[l1+1] = 0; 
   /*extern weight */      printf(" DIRC3 = %s \n",dirc);
   /* We are differentiating ll according to initial status */    }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    ss = strrchr( name, '.' );            /* find last / */
   /*for(i=1;i<imx;i++)    if (ss >0){
     printf(" %d\n",s[4][i]);      ss++;
   */      strcpy(ext,ss);                     /* save extension */
   cov[1]=1.;      l1= strlen( name);
       l2= strlen(ss)+1;
   for(k=1; k<=nlstate; k++) ll[k]=0.;      strncpy( finame, name, l1-l2);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      finame[l1-l2]= 0;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    }
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)    return( 0 );                          /* we're done */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  }
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /******************************************/
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  void replace_back_to_slash(char *s, char*t)
         }  {
            int i;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    int lg=0;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    i=0;
         savm=oldm;    lg=strlen(t);
         oldm=newm;    for(i=0; i<= lg; i++) {
              (s[i] = t[i]);
              if (t[i]== '\\') s[i]='/';
       } /* end mult */    }
        }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  char *trimbb(char *out, char *in)
       ipmx +=1;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       sw += weight[i];    char *s;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    s=out;
     } /* end of wave */    while (*in != '\0'){
   } /* end of individual */      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         in++;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      *out++ = *in++;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    }
   return -l;    *out='\0';
 }    return s;
   }
   
 /*********** Maximum Likelihood Estimation ***************/  char *cutl(char *blocc, char *alocc, char *in, char occ)
   {
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
 {       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   int i,j, iter;       gives blocc="abcdef2ghi" and alocc="j".
   double **xi,*delti;       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   double fret;    */
   xi=matrix(1,npar,1,npar);    char *s, *t;
   for (i=1;i<=npar;i++)    t=in;s=in;
     for (j=1;j<=npar;j++)    while ((*in != occ) && (*in != '\0')){
       xi[i][j]=(i==j ? 1.0 : 0.0);      *alocc++ = *in++;
   printf("Powell\n");    }
   powell(p,xi,npar,ftol,&iter,&fret,func);    if( *in == occ){
       *(alocc)='\0';
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      s=++in;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    }
    
 }    if (s == t) {/* occ not found */
       *(alocc-(in-s))='\0';
 /**** Computes Hessian and covariance matrix ***/      in=s;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    }
 {    while ( *in != '\0'){
   double  **a,**y,*x,pd;      *blocc++ = *in++;
   double **hess;    }
   int i, j,jk;  
   int *indx;    *blocc='\0';
     return t;
   double hessii(double p[], double delta, int theta, double delti[]);  }
   double hessij(double p[], double delti[], int i, int j);  char *cutv(char *blocc, char *alocc, char *in, char occ)
   void lubksb(double **a, int npar, int *indx, double b[]) ;  {
   void ludcmp(double **a, int npar, int *indx, double *d) ;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
        and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   hess=matrix(1,npar,1,npar);       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
   printf("\nCalculation of the hessian matrix. Wait...\n");    */
   for (i=1;i<=npar;i++){    char *s, *t;
     printf("%d",i);fflush(stdout);    t=in;s=in;
     hess[i][i]=hessii(p,ftolhess,i,delti);    while (*in != '\0'){
     /*printf(" %f ",p[i]);*/      while( *in == occ){
     /*printf(" %lf ",hess[i][i]);*/        *blocc++ = *in++;
   }        s=in;
        }
   for (i=1;i<=npar;i++) {      *blocc++ = *in++;
     for (j=1;j<=npar;j++)  {    }
       if (j>i) {    if (s == t) /* occ not found */
         printf(".%d%d",i,j);fflush(stdout);      *(blocc-(in-s))='\0';
         hess[i][j]=hessij(p,delti,i,j);    else
         hess[j][i]=hess[i][j];          *(blocc-(in-s)-1)='\0';
         /*printf(" %lf ",hess[i][j]);*/    in=s;
       }    while ( *in != '\0'){
     }      *alocc++ = *in++;
   }    }
   printf("\n");  
     *alocc='\0';
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    return s;
    }
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);  int nbocc(char *s, char occ)
   x=vector(1,npar);  {
   indx=ivector(1,npar);    int i,j=0;
   for (i=1;i<=npar;i++)    int lg=20;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    i=0;
   ludcmp(a,npar,indx,&pd);    lg=strlen(s);
     for(i=0; i<= lg; i++) {
   for (j=1;j<=npar;j++) {    if  (s[i] == occ ) j++;
     for (i=1;i<=npar;i++) x[i]=0;    }
     x[j]=1;    return j;
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];  /* void cutv(char *u,char *v, char*t, char occ) */
     }  /* { */
   }  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   printf("\n#Hessian matrix#\n");  /*      gives u="abcdef2ghi" and v="j" *\/ */
   for (i=1;i<=npar;i++) {  /*   int i,lg,j,p=0; */
     for (j=1;j<=npar;j++) {  /*   i=0; */
       printf("%.3e ",hess[i][j]);  /*   lg=strlen(t); */
     }  /*   for(j=0; j<=lg-1; j++) { */
     printf("\n");  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   }  /*   } */
   
   /* Recompute Inverse */  /*   for(j=0; j<p; j++) { */
   for (i=1;i<=npar;i++)  /*     (u[j] = t[j]); */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /*   } */
   ludcmp(a,npar,indx,&pd);  /*      u[p]='\0'; */
   
   /*  printf("\n#Hessian matrix recomputed#\n");  /*    for(j=0; j<= lg; j++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   for (j=1;j<=npar;j++) {  /*   } */
     for (i=1;i<=npar;i++) x[i]=0;  /* } */
     x[j]=1;  
     lubksb(a,npar,indx,x);  #ifdef _WIN32
     for (i=1;i<=npar;i++){  char * strsep(char **pp, const char *delim)
       y[i][j]=x[i];  {
       printf("%.3e ",y[i][j]);    char *p, *q;
     }           
     printf("\n");    if ((p = *pp) == NULL)
   }      return 0;
   */    if ((q = strpbrk (p, delim)) != NULL)
     {
   free_matrix(a,1,npar,1,npar);      *pp = q + 1;
   free_matrix(y,1,npar,1,npar);      *q = '\0';
   free_vector(x,1,npar);    }
   free_ivector(indx,1,npar);    else
   free_matrix(hess,1,npar,1,npar);      *pp = 0;
     return p;
   }
 }  #endif
   
 /*************** hessian matrix ****************/  /********************** nrerror ********************/
 double hessii( double x[], double delta, int theta, double delti[])  
 {  void nrerror(char error_text[])
   int i;  {
   int l=1, lmax=20;    fprintf(stderr,"ERREUR ...\n");
   double k1,k2;    fprintf(stderr,"%s\n",error_text);
   double p2[NPARMAX+1];    exit(EXIT_FAILURE);
   double res;  }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /*********************** vector *******************/
   double fx;  double *vector(int nl, int nh)
   int k=0,kmax=10;  {
   double l1;    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   fx=func(x);    if (!v) nrerror("allocation failure in vector");
   for (i=1;i<=npar;i++) p2[i]=x[i];    return v-nl+NR_END;
   for(l=0 ; l <=lmax; l++){  }
     l1=pow(10,l);  
     delts=delt;  /************************ free vector ******************/
     for(k=1 ; k <kmax; k=k+1){  void free_vector(double*v, int nl, int nh)
       delt = delta*(l1*k);  {
       p2[theta]=x[theta] +delt;    free((FREE_ARG)(v+nl-NR_END));
       k1=func(p2)-fx;  }
       p2[theta]=x[theta]-delt;  
       k2=func(p2)-fx;  /************************ivector *******************************/
       /*res= (k1-2.0*fx+k2)/delt/delt; */  int *ivector(long nl,long nh)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  {
          int *v;
 #ifdef DEBUG    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       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);    if (!v) nrerror("allocation failure in ivector");
 #endif    return v-nl+NR_END;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;  /******************free ivector **************************/
       }  void free_ivector(int *v, long nl, long nh)
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  {
         k=kmax; l=lmax*10.;    free((FREE_ARG)(v+nl-NR_END));
       }  }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  /************************lvector *******************************/
       }  long *lvector(long nl,long nh)
     }  {
   }    long *v;
   delti[theta]=delts;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   return res;    if (!v) nrerror("allocation failure in ivector");
      return v-nl+NR_END;
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  /******************free lvector **************************/
 {  void free_lvector(long *v, long nl, long nh)
   int i;  {
   int l=1, l1, lmax=20;    free((FREE_ARG)(v+nl-NR_END));
   double k1,k2,k3,k4,res,fx;  }
   double p2[NPARMAX+1];  
   int k;  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
   fx=func(x);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   for (k=1; k<=2; k++) {  { 
     for (i=1;i<=npar;i++) p2[i]=x[i];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    int **m; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    
     k1=func(p2)-fx;    /* allocate pointers to rows */ 
      m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     p2[thetai]=x[thetai]+delti[thetai]/k;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    m += NR_END; 
     k2=func(p2)-fx;    m -= nrl; 
      
     p2[thetai]=x[thetai]-delti[thetai]/k;    
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    /* allocate rows and set pointers to them */ 
     k3=func(p2)-fx;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     p2[thetai]=x[thetai]-delti[thetai]/k;    m[nrl] += NR_END; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    m[nrl] -= ncl; 
     k4=func(p2)-fx;    
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 #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);    /* return pointer to array of pointers to rows */ 
 #endif    return m; 
   }  } 
   return res;  
 }  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
 /************** Inverse of matrix **************/        int **m;
 void ludcmp(double **a, int n, int *indx, double *d)        long nch,ncl,nrh,nrl; 
 {       /* free an int matrix allocated by imatrix() */ 
   int i,imax,j,k;  { 
   double big,dum,sum,temp;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double *vv;    free((FREE_ARG) (m+nrl-NR_END)); 
    } 
   vv=vector(1,n);  
   *d=1.0;  /******************* matrix *******************************/
   for (i=1;i<=n;i++) {  double **matrix(long nrl, long nrh, long ncl, long nch)
     big=0.0;  {
     for (j=1;j<=n;j++)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       if ((temp=fabs(a[i][j])) > big) big=temp;    double **m;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
   for (j=1;j<=n;j++) {    m += NR_END;
     for (i=1;i<j;i++) {    m -= nrl;
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       a[i][j]=sum;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     big=0.0;    m[nrl] -= ncl;
     for (i=j;i<=n;i++) {  
       sum=a[i][j];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for (k=1;k<j;k++)    return m;
         sum -= a[i][k]*a[k][j];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
       a[i][j]=sum;  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
       if ( (dum=vv[i]*fabs(sum)) >= big) {  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
         big=dum;     */
         imax=i;  }
       }  
     }  /*************************free matrix ************************/
     if (j != imax) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       for (k=1;k<=n;k++) {  {
         dum=a[imax][k];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         a[imax][k]=a[j][k];    free((FREE_ARG)(m+nrl-NR_END));
         a[j][k]=dum;  }
       }  
       *d = -(*d);  /******************* ma3x *******************************/
       vv[imax]=vv[j];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     }  {
     indx[j]=imax;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     if (a[j][j] == 0.0) a[j][j]=TINY;    double ***m;
     if (j != n) {  
       dum=1.0/(a[j][j]);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
   }    m -= nrl;
   free_vector(vv,1,n);  /* Doesn't work */  
 ;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 void lubksb(double **a, int n, int *indx, double b[])    m[nrl] -= ncl;
 {  
   int i,ii=0,ip,j;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double sum;  
      m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for (i=1;i<=n;i++) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     ip=indx[i];    m[nrl][ncl] += NR_END;
     sum=b[ip];    m[nrl][ncl] -= nll;
     b[ip]=b[i];    for (j=ncl+1; j<=nch; j++) 
     if (ii)      m[nrl][j]=m[nrl][j-1]+nlay;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    
     else if (sum) ii=i;    for (i=nrl+1; i<=nrh; i++) {
     b[i]=sum;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   }      for (j=ncl+1; j<=nch; j++) 
   for (i=n;i>=1;i--) {        m[i][j]=m[i][j-1]+nlay;
     sum=b[i];    }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    return m; 
     b[i]=sum/a[i][i];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 }    */
   }
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1,double **mint,double **anint)  /*************************free ma3x ************************/
 {  /* Some frequencies */  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
    {
   int i, m, jk, k1, k2,i1, j1, bool, z1,z2,j;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double ***freq; /* Frequencies */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double *pp;    free((FREE_ARG)(m+nrl-NR_END));
   double pos;  }
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
   pp=vector(1,nlstate);  {
   probs= ma3x(1,130 ,1,8, 1,8);    /* Caution optionfilefiname is hidden */
   strcpy(fileresp,"p");    strcpy(tmpout,optionfilefiname);
   strcat(fileresp,fileres);    strcat(tmpout,"/"); /* Add to the right */
   if((ficresp=fopen(fileresp,"w"))==NULL) {    strcat(tmpout,fileres);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    return tmpout;
     exit(0);  }
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*************** function subdirf2 ***********/
   j1=0;  char *subdirf2(char fileres[], char *preop)
   {
   j=cptcoveff;    
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   for(k1=1; k1<=j;k1++){    strcat(tmpout,"/");
    for(i1=1; i1<=ncodemax[k1];i1++){    strcat(tmpout,preop);
        j1++;    strcat(tmpout,fileres);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    return tmpout;
          scanf("%d", i);*/  }
         for (i=-1; i<=nlstate+ndeath; i++)    
          for (jk=-1; jk<=nlstate+ndeath; jk++)    /*************** function subdirf3 ***********/
            for(m=agemin; m <= agemax+3; m++)  char *subdirf3(char fileres[], char *preop, char *preop2)
              freq[i][jk][m]=0;  {
            
        for (i=1; i<=imx; i++) {    /* Caution optionfilefiname is hidden */
          bool=1;    strcpy(tmpout,optionfilefiname);
          if  (cptcovn>0) {    strcat(tmpout,"/");
            for (z1=1; z1<=cptcoveff; z1++)    strcat(tmpout,preop);
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    strcat(tmpout,preop2);
                bool=0;    strcat(tmpout,fileres);
          }    return tmpout;
           if (bool==1) {  }
             for(m=fprev1; m<=lprev1; m++){  
              k2=anint[m][i]+(mint[m][i]/12.);  char *asc_diff_time(long time_sec, char ascdiff[])
              if ((k2>=1984) && (k2<=1988.5)) {  {
              if(agev[m][i]==0) agev[m][i]=agemax+1;    long sec_left, days, hours, minutes;
              if(agev[m][i]==1) agev[m][i]=agemax+2;    days = (time_sec) / (60*60*24);
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    sec_left = (time_sec) % (60*60*24);
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    hours = (sec_left) / (60*60) ;
              }    sec_left = (sec_left) %(60*60);
             }    minutes = (sec_left) /60;
           }    sec_left = (sec_left) % (60);
        }    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
         if  (cptcovn>0) {    return ascdiff;
          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#");  /***************** f1dim *************************/
         }  extern int ncom; 
        for(i=1; i<=nlstate;i++)  extern double *pcom,*xicom;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  extern double (*nrfunc)(double []); 
        fprintf(ficresp, "\n");   
          double f1dim(double x) 
   for(i=(int)agemin; i <= (int)agemax+3; i++){  { 
     if(i==(int)agemax+3)    int j; 
       printf("Total");    double f;
     else    double *xt; 
       printf("Age %d", i);   
     for(jk=1; jk <=nlstate ; jk++){    xt=vector(1,ncom); 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         pp[jk] += freq[jk][m][i];    f=(*nrfunc)(xt); 
     }    free_vector(xt,1,ncom); 
     for(jk=1; jk <=nlstate ; jk++){    return f; 
       for(m=-1, pos=0; m <=0 ; m++)  } 
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)  /*****************brent *************************/
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       else  { 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    int iter; 
     }    double a,b,d,etemp;
     double fu=0,fv,fw,fx;
      for(jk=1; jk <=nlstate ; jk++){    double ftemp=0.;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         pp[jk] += freq[jk][m][i];    double e=0.0; 
      }   
     a=(ax < cx ? ax : cx); 
     for(jk=1,pos=0; jk <=nlstate ; jk++)    b=(ax > cx ? ax : cx); 
       pos += pp[jk];    x=w=v=bx; 
     for(jk=1; jk <=nlstate ; jk++){    fw=fv=fx=(*f)(x); 
       if(pos>=1.e-5)    for (iter=1;iter<=ITMAX;iter++) { 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      xm=0.5*(a+b); 
       else      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       if( i <= (int) agemax){      printf(".");fflush(stdout);
         if(pos>=1.e-5){      fprintf(ficlog,".");fflush(ficlog);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  #ifdef DEBUGBRENT
           probs[i][jk][j1]= pp[jk]/pos;      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);
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       else  #endif
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       }        *xmin=x; 
     }        return fx; 
     for(jk=-1; jk <=nlstate+ndeath; jk++)      } 
       for(m=-1; m <=nlstate+ndeath; m++)      ftemp=fu;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      if (fabs(e) > tol1) { 
     if(i <= (int) agemax)        r=(x-w)*(fx-fv); 
       fprintf(ficresp,"\n");        q=(x-v)*(fx-fw); 
     printf("\n");        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
     }        if (q > 0.0) p = -p; 
  }        q=fabs(q); 
          etemp=e; 
   fclose(ficresp);        e=d; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   free_vector(pp,1,nlstate);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
 }  /* End of Freq */          d=p/q; 
           u=x+d; 
 /************ Prevalence ********************/          if (u-a < tol2 || b-u < tol2) 
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)            d=SIGN(tol1,xm-x); 
 {  /* Some frequencies */        } 
        } else { 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double ***freq; /* Frequencies */      } 
   double *pp;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double pos;      fu=(*f)(u); 
       if (fu <= fx) { 
   pp=vector(1,nlstate);        if (u >= x) a=x; else b=x; 
   probs= ma3x(1,130 ,1,8, 1,8);        SHFT(v,w,x,u) 
            SHFT(fv,fw,fx,fu) 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          } else { 
   j1=0;            if (u < x) a=u; else b=u; 
              if (fu <= fw || w == x) { 
   j=cptcoveff;              v=w; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}              w=u; 
                fv=fw; 
  for(k1=1; k1<=j;k1++){              fw=fu; 
     for(i1=1; i1<=ncodemax[k1];i1++){            } else if (fu <= fv || v == x || v == w) { 
       j1++;              v=u; 
                fv=fu; 
       for (i=-1; i<=nlstate+ndeath; i++)              } 
         for (jk=-1; jk<=nlstate+ndeath; jk++)            } 
           for(m=agemin; m <= agemax+3; m++)    } 
           freq[i][jk][m]=0;    nrerror("Too many iterations in brent"); 
          *xmin=x; 
       for (i=1; i<=imx; i++) {    return fx; 
         bool=1;  } 
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  /****************** mnbrak ***********************/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               }              double (*func)(double)) 
         if (bool==1) {  { 
           for(m=fprev1; m<=lprev1; m++){    double ulim,u,r,q, dum;
             if(agev[m][i]==0) agev[m][i]=agemax+1;    double fu; 
             if(agev[m][i]==1) agev[m][i]=agemax+2;   
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    *fa=(*func)(*ax); 
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    *fb=(*func)(*bx); 
           }    if (*fb > *fa) { 
         }      SHFT(dum,*ax,*bx,dum) 
       }        SHFT(dum,*fb,*fa,dum) 
        for(i=(int)agemin; i <= (int)agemax+3; i++){        } 
         for(jk=1; jk <=nlstate ; jk++){    *cx=(*bx)+GOLD*(*bx-*ax); 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    *fc=(*func)(*cx); 
             pp[jk] += freq[jk][m][i];    while (*fb > *fc) { /* Declining fa, fb, fc */
         }      r=(*bx-*ax)*(*fb-*fc); 
         for(jk=1; jk <=nlstate ; jk++){      q=(*bx-*cx)*(*fb-*fa); 
           for(m=-1, pos=0; m <=0 ; m++)      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
             pos += freq[jk][m][i];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
         }      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
              if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
          for(jk=1; jk <=nlstate ; jk++){        fu=(*func)(u); 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  #ifdef DEBUG
              pp[jk] += freq[jk][m][i];        /* f(x)=A(x-u)**2+f(u) */
          }        double A, fparabu; 
                  A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        fparabu= *fa - A*(*ax-u)*(*ax-u);
         printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
          for(jk=1; jk <=nlstate ; jk++){                  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);
            if( i <= (int) agemax){  #endif 
              if(pos>=1.e-5){      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
                probs[i][jk][j1]= pp[jk]/pos;        fu=(*func)(u); 
              }        if (fu < *fc) { 
            }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
          }            SHFT(*fb,*fc,fu,(*func)(u)) 
                      } 
          }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
     }        u=ulim; 
   }        fu=(*func)(u); 
        } else { 
          u=(*cx)+GOLD*(*cx-*bx); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        fu=(*func)(u); 
   free_vector(pp,1,nlstate);      } 
        SHFT(*ax,*bx,*cx,u) 
 }  /* End of Freq */        SHFT(*fa,*fb,*fc,fu) 
 /************* Waves Concatenation ***************/        } 
   } 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {  /*************** linmin ************************/
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
      Death is a valid wave (if date is known).  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  the value of func at the returned location p . This is actually all accomplished by calling the
      and mw[mi+1][i]. dh depends on stepm.  routines mnbrak and brent .*/
      */  int ncom; 
   double *pcom,*xicom;
   int i, mi, m;  double (*nrfunc)(double []); 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;   
      double sum=0., jmean=0.;*/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
   int j, k=0,jk, ju, jl;    double brent(double ax, double bx, double cx, 
   double sum=0.;                 double (*f)(double), double tol, double *xmin); 
   jmin=1e+5;    double f1dim(double x); 
   jmax=-1;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   jmean=0.;                double *fc, double (*func)(double)); 
   for(i=1; i<=imx; i++){    int j; 
     mi=0;    double xx,xmin,bx,ax; 
     m=firstpass;    double fx,fb,fa;
     while(s[m][i] <= nlstate){   
       if(s[m][i]>=1)    ncom=n; 
         mw[++mi][i]=m;    pcom=vector(1,n); 
       if(m >=lastpass)    xicom=vector(1,n); 
         break;    nrfunc=func; 
       else    for (j=1;j<=n;j++) { 
         m++;      pcom[j]=p[j]; 
     }/* end while */      xicom[j]=xi[j]; 
     if (s[m][i] > nlstate){    } 
       mi++;     /* Death is another wave */    ax=0.0; 
       /* if(mi==0)  never been interviewed correctly before death */    xx=1.0; 
          /* Only death is a correct wave */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
       mw[mi][i]=m;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
     }  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     wav[i]=mi;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if(mi==0)  #endif
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    for (j=1;j<=n;j++) { 
   }      xi[j] *= xmin; 
       p[j] += xi[j]; 
   for(i=1; i<=imx; i++){    } 
     for(mi=1; mi<wav[i];mi++){    free_vector(xicom,1,n); 
       if (stepm <=0)    free_vector(pcom,1,n); 
         dh[mi][i]=1;  } 
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  /*************** powell ************************/
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  /*
           if(j==0) j=1;  /* Survives at least one month after exam */  Minimization of a function func of n variables. Input consists of an initial starting point
           k=k+1;  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
           if (j >= jmax) jmax=j;  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
           if (j <= jmin) jmin=j;  such that failure to decrease by more than this amount on one iteration signals doneness. On
           sum=sum+j;  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
           /* if (j<10) printf("j=%d num=%d ",j,i); */  function value at p , and iter is the number of iterations taken. The routine linmin is used.
           }   */
         }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         else{              double (*func)(double [])) 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  { 
           k=k+1;    void linmin(double p[], double xi[], int n, double *fret, 
           if (j >= jmax) jmax=j;                double (*func)(double [])); 
           else if (j <= jmin)jmin=j;    int i,ibig,j; 
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    double del,t,*pt,*ptt,*xit;
           sum=sum+j;    double directest;
         }    double fp,fptt;
         jk= j/stepm;    double *xits;
         jl= j -jk*stepm;    int niterf, itmp;
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)    pt=vector(1,n); 
           dh[mi][i]=jk;    ptt=vector(1,n); 
         else    xit=vector(1,n); 
           dh[mi][i]=jk+1;    xits=vector(1,n); 
         if(dh[mi][i]==0)    *fret=(*func)(p); 
           dh[mi][i]=1; /* At least one step */    for (j=1;j<=n;j++) pt[j]=p[j]; 
       }      rcurr_time = time(NULL);  
     }    for (*iter=1;;++(*iter)) { 
   }      fp=(*fret); 
   jmean=sum/k;      ibig=0; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      del=0.0; 
  }      rlast_time=rcurr_time;
 /*********** Tricode ****************************/      /* (void) gettimeofday(&curr_time,&tzp); */
 void tricode(int *Tvar, int **nbcode, int imx)      rcurr_time = time(NULL);  
 {      curr_time = *localtime(&rcurr_time);
   int Ndum[20],ij=1, k, j, i;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
   int cptcode=0;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   cptcoveff=0;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
       for (i=1;i<=n;i++) {
   for (k=0; k<19; k++) Ndum[k]=0;        printf(" %d %.12f",i, p[i]);
   for (k=1; k<=7; k++) ncodemax[k]=0;        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      }
     for (i=1; i<=imx; i++) {      printf("\n");
       ij=(int)(covar[Tvar[j]][i]);      fprintf(ficlog,"\n");
       Ndum[ij]++;      fprintf(ficrespow,"\n");fflush(ficrespow);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      if(*iter <=3){
       if (ij > cptcode) cptcode=ij;        tml = *localtime(&rcurr_time);
     }        strcpy(strcurr,asctime(&tml));
         rforecast_time=rcurr_time; 
     for (i=0; i<=cptcode; i++) {        itmp = strlen(strcurr);
       if(Ndum[i]!=0) ncodemax[j]++;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     }          strcurr[itmp-1]='\0';
     ij=1;        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         for(niterf=10;niterf<=30;niterf+=10){
     for (i=1; i<=ncodemax[j]; i++) {          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
       for (k=0; k<=19; k++) {          forecast_time = *localtime(&rforecast_time);
         if (Ndum[k] != 0) {          strcpy(strfor,asctime(&forecast_time));
           nbcode[Tvar[j]][ij]=k;          itmp = strlen(strfor);
           ij++;          if(strfor[itmp-1]=='\n')
         }          strfor[itmp-1]='\0';
         if (ij > ncodemax[j]) break;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }            fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
     }        }
   }        }
       for (i=1;i<=n;i++) { 
  for (k=0; k<19; k++) Ndum[k]=0;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
  for (i=1; i<=ncovmodel-2; i++) {  #ifdef DEBUG
       ij=Tvar[i];            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       Ndum[ij]++;            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     }  #endif
         printf("%d",i);fflush(stdout);
  ij=1;        fprintf(ficlog,"%d",i);fflush(ficlog);
  for (i=1; i<=10; i++) {        linmin(p,xit,n,fret,func); 
    if((Ndum[i]!=0) && (i<=ncov)){        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
      Tvaraff[ij]=i;                                         because that direction will be replaced unless the gain del is small
      ij++;                                        in comparison with the 'probable' gain, mu^2, with the last average direction.
    }                                        Unless the n directions are conjugate some gain in the determinant may be obtained
  }                                        with the new direction.
                                          */
     cptcoveff=ij-1;          del=fabs(fptt-(*fret)); 
 }          ibig=i; 
         } 
 /*********** Health Expectancies ****************/  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        fprintf(ficlog,"%d %.12e",i,(*fret));
 {        for (j=1;j<=n;j++) {
   /* Health expectancies */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   int i, j, nhstepm, hstepm, h;          printf(" x(%d)=%.12e",j,xit[j]);
   double age, agelim,hf;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double ***p3mat;        }
          for(j=1;j<=n;j++) {
   fprintf(ficreseij,"# Health expectancies\n");          printf(" p(%d)=%.12e",j,p[j]);
   fprintf(ficreseij,"# Age");          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
   for(i=1; i<=nlstate;i++)        }
     for(j=1; j<=nlstate;j++)        printf("\n");
       fprintf(ficreseij," %1d-%1d",i,j);        fprintf(ficlog,"\n");
   fprintf(ficreseij,"\n");  #endif
       } /* end i */
   hstepm=1*YEARM; /*  Every j years of age (in month) */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  #ifdef DEBUG
         int k[2],l;
   agelim=AGESUP;        k[0]=1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        k[1]=-1;
     /* nhstepm age range expressed in number of stepm */        printf("Max: %.12e",(*func)(p));
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        fprintf(ficlog,"Max: %.12e",(*func)(p));
     /* Typically if 20 years = 20*12/6=40 stepm */        for (j=1;j<=n;j++) {
     if (stepm >= YEARM) hstepm=1;          printf(" %.12e",p[j]);
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          fprintf(ficlog," %.12e",p[j]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        printf("\n");
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        fprintf(ficlog,"\n");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for(i=1; i<=nlstate;i++)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for(j=1; j<=nlstate;j++)            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          }
           eij[i][j][(int)age] +=p3mat[i][j][h];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
            }
     hf=1;  #endif
     if (stepm >= YEARM) hf=stepm/YEARM;  
     fprintf(ficreseij,"%.0f",age );  
     for(i=1; i<=nlstate;i++)        free_vector(xit,1,n); 
       for(j=1; j<=nlstate;j++){        free_vector(xits,1,n); 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
     fprintf(ficreseij,"\n");        return; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } 
   }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
         ptt[j]=2.0*p[j]-pt[j]; 
 /************ Variance ******************/        xit[j]=p[j]-pt[j]; 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        pt[j]=p[j]; 
 {      } 
   /* Variance of health expectancies */      fptt=(*func)(ptt); /* f_3 */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   double **newm;        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
   double **dnewm,**doldm;        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
   int i, j, nhstepm, hstepm, h;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
   int k, cptcode;        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   double *xp;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
   double **gp, **gm;        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
   double ***gradg, ***trgradg;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   double ***p3mat;  
   double age,agelim;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
   int theta;        t= t- del*SQR(fp-fptt);
         directest = SQR(fp-2.0*(*fret)+fptt) - 2.0 * del; /* If del was big enough we change it for a new direction */
    fprintf(ficresvij,"# Covariances of life expectancies\n");  #ifdef DEBUG
   fprintf(ficresvij,"# Age");        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(i=1; i<=nlstate;i++)        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);
     for(j=1; j<=nlstate;j++)        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   fprintf(ficresvij,"\n");        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));
   xp=vector(1,npar);        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);
   dnewm=matrix(1,nlstate,1,npar);        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);
   doldm=matrix(1,nlstate,1,nlstate);  #endif
    #ifdef POWELLDIRECT
   hstepm=1*YEARM; /* Every year of age */        if (directest < 0.0) { /* Then we use it for new direction */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  #else
   agelim = AGESUP;        if (t < 0.0) { /* Then we use it for new direction */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #endif
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
     if (stepm >= YEARM) hstepm=1;          for (j=1;j<=n;j++) { 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          }
     gp=matrix(0,nhstepm,1,nlstate);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     gm=matrix(0,nhstepm,1,nlstate);          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   
     for(theta=1; theta <=npar; theta++){  #ifdef DEBUG
       for(i=1; i<=npar; i++){ /* Computes gradient */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       }          for(j=1;j<=n;j++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              printf(" %.12e",xit[j]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            fprintf(ficlog," %.12e",xit[j]);
           }
       if (popbased==1) {          printf("\n");
         for(i=1; i<=nlstate;i++)          fprintf(ficlog,"\n");
           prlim[i][i]=probs[(int)age][i][ij];  #endif
       }        } /* end of t negative */
            } /* end if (fptt < fp)  */
       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];  /**** Prevalence limit (stable or period prevalence)  ****************/
         }  
       }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
      {
       for(i=1; i<=npar; i++) /* Computes gradient */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       matrix by transitions matrix until convergence is reached */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
       if (popbased==1) {    /* double **matprod2(); */ /* test */
         for(i=1; i<=nlstate;i++)    double **out, cov[NCOVMAX+1], **pmij();
           prlim[i][i]=probs[(int)age][i][ij];    double **newm;
       }    double agefin, delaymax=50 ; /* Max number of years to converge */
     
       for(j=1; j<= nlstate; j++){    for (ii=1;ii<=nlstate+ndeath;ii++)
         for(h=0; h<=nhstepm; h++){      for (j=1;j<=nlstate+ndeath;j++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      }
         }    
       }    cov[1]=1.;
     
       for(j=1; j<= nlstate; j++)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         for(h=0; h<=nhstepm; h++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      newm=savm;
         }      /* Covariates have to be included here again */
     } /* End theta */      cov[2]=agefin;
       
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (k=1; k<=cptcovn;k++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for(h=0; h<=nhstepm; h++)        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
       for(j=1; j<=nlstate;j++)      }
         for(theta=1; theta <=npar; theta++)      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           trgradg[h][j][theta]=gradg[h][theta][j];      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
       /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
     for(i=1;i<=nlstate;i++)      
       for(j=1;j<=nlstate;j++)      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         vareij[i][j][(int)age] =0.;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for(h=0;h<=nhstepm;h++){      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for(k=0;k<=nhstepm;k++){      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
         for(i=1;i<=nlstate;i++)      
           for(j=1;j<=nlstate;j++)      savm=oldm;
             vareij[i][j][(int)age] += doldm[i][j];      oldm=newm;
       }      maxmax=0.;
     }      for(j=1;j<=nlstate;j++){
     h=1;        min=1.;
     if (stepm >= YEARM) h=stepm/YEARM;        max=0.;
     fprintf(ficresvij,"%.0f ",age );        for(i=1; i<=nlstate; i++) {
     for(i=1; i<=nlstate;i++)          sumnew=0;
       for(j=1; j<=nlstate;j++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          prlim[i][j]= newm[i][j]/(1-sumnew);
       }          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
     fprintf(ficresvij,"\n");          max=FMAX(max,prlim[i][j]);
     free_matrix(gp,0,nhstepm,1,nlstate);          min=FMIN(min,prlim[i][j]);
     free_matrix(gm,0,nhstepm,1,nlstate);        }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        maxmin=max-min;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        maxmax=FMAX(maxmax,maxmin);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* j loop */
   } /* End age */      if(maxmax < ftolpl){
          return prlim;
   free_vector(xp,1,npar);      }
   free_matrix(doldm,1,nlstate,1,npar);    } /* age loop */
   free_matrix(dnewm,1,nlstate,1,nlstate);    return prlim; /* should not reach here */
   }
 }  
   /*************** transition probabilities ***************/ 
 /************ 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)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   /* Variance of prevalence limit */    /* According to parameters values stored in x and the covariate's values stored in cov,
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       computes the probability to be observed in state j being in state i by appying the
   double **newm;       model to the ncovmodel covariates (including constant and age).
   double **dnewm,**doldm;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   int i, j, nhstepm, hstepm;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   int k, cptcode;       ncth covariate in the global vector x is given by the formula:
   double *xp;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   double *gp, *gm;       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   double **gradg, **trgradg;       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
   double age,agelim;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   int theta;       Outputs ps[i][j] the probability to be observed in j being in j according to
           the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    */
   fprintf(ficresvpl,"# Age");    double s1, lnpijopii;
   for(i=1; i<=nlstate;i++)    /*double t34;*/
       fprintf(ficresvpl," %1d-%1d",i,i);    int i,j, nc, ii, jj;
   fprintf(ficresvpl,"\n");  
       for(i=1; i<= nlstate; i++){
   xp=vector(1,npar);        for(j=1; j<i;j++){
   dnewm=matrix(1,nlstate,1,npar);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   doldm=matrix(1,nlstate,1,nlstate);            /*lnpijopii += param[i][j][nc]*cov[nc];*/
              lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   hstepm=1*YEARM; /* Every year of age */  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          }
   agelim = AGESUP;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
     if (stepm >= YEARM) hstepm=1;        for(j=i+1; j<=nlstate+ndeath;j++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     gradg=matrix(1,npar,1,nlstate);            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     gp=vector(1,nlstate);            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     gm=vector(1,nlstate);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
           }
     for(theta=1; theta <=npar; theta++){          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       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++){
       for(i=1;i<=nlstate;i++)        s1=0;
         gp[i] = prlim[i][i];        for(j=1; j<i; j++){
              s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       for(i=1; i<=npar; i++) /* Computes gradient */          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(j=i+1; j<=nlstate+ndeath; j++){
       for(i=1;i<=nlstate;i++)          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         gm[i] = prlim[i][i];          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
       for(i=1;i<=nlstate;i++)        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        ps[i][i]=1./(s1+1.);
     } /* End theta */        /* Computing other pijs */
         for(j=1; j<i; j++)
     trgradg =matrix(1,nlstate,1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
     for(j=1; j<=nlstate;j++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(theta=1; theta <=npar; theta++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         trgradg[j][theta]=gradg[theta][j];      } /* end i */
       
     for(i=1;i<=nlstate;i++)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       varpl[i][(int)age] =0.;        for(jj=1; jj<= nlstate+ndeath; jj++){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          ps[ii][jj]=0;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          ps[ii][ii]=1;
     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++)      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     fprintf(ficresvpl,"\n");      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     free_vector(gp,1,nlstate);      /*   } */
     free_vector(gm,1,nlstate);      /*   printf("\n "); */
     free_matrix(gradg,1,npar,1,nlstate);      /* } */
     free_matrix(trgradg,1,nlstate,1,npar);      /* printf("\n ");printf("%lf ",cov[2]);*/
   } /* End age */      /*
         for(i=1; i<= npar; i++) printf("%f ",x[i]);
   free_vector(xp,1,npar);        goto end;*/
   free_matrix(doldm,1,nlstate,1,npar);      return ps;
   free_matrix(dnewm,1,nlstate,1,nlstate);  }
   
 }  /**************** Product of 2 matrices ******************/
   
 /************ Variance of one-step probabilities  ******************/  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  {
 {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   int i, j;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   int k=0, cptcode;    /* in, b, out are matrice of pointers which should have been initialized 
   double **dnewm,**doldm;       before: only the contents of out is modified. The function returns
   double *xp;       a pointer to pointers identical to out */
   double *gp, *gm;    int i, j, k;
   double **gradg, **trgradg;    for(i=nrl; i<= nrh; i++)
   double age,agelim, cov[NCOVMAX];      for(k=ncolol; k<=ncoloh; k++){
   int theta;        out[i][k]=0.;
   char fileresprob[FILENAMELENGTH];        for(j=ncl; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
   strcpy(fileresprob,"prob");      }
   strcat(fileresprob,fileres);    return out;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  }
     printf("Problem with resultfile: %s\n", fileresprob);  
   }  
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  /************* Higher Matrix Product ***************/
    
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   xp=vector(1,npar);  {
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* Computes the transition matrix starting at age 'age' over 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));       'nhstepm*hstepm*stepm' months (i.e. until
         age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   cov[1]=1;       nhstepm*hstepm matrices. 
   for (age=bage; age<=fage; age ++){       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     cov[2]=age;       (typically every 2 years instead of every month which is too big 
     gradg=matrix(1,npar,1,9);       for the memory).
     trgradg=matrix(1,9,1,npar);       Model is determined by parameters x and covariates have to be 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));       included manually here. 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
           */
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++)    int i, j, d, h, k;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double **out, cov[NCOVMAX+1];
          double **newm;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
        /* Hstepm could be zero and should return the unit matrix */
       k=0;    for (i=1;i<=nlstate+ndeath;i++)
       for(i=1; i<= (nlstate+ndeath); i++){      for (j=1;j<=nlstate+ndeath;j++){
         for(j=1; j<=(nlstate+ndeath);j++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
            k=k+1;        po[i][j][0]=(i==j ? 1.0 : 0.0);
           gp[k]=pmmij[i][j];      }
         }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       }    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
       for(i=1; i<=npar; i++)        newm=savm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        /* Covariates have to be included here again */
            cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        for (k=1; k<=cptcovn;k++) 
       k=0;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for(i=1; i<=(nlstate+ndeath); i++){        for (k=1; k<=cptcovage;k++)
         for(j=1; j<=(nlstate+ndeath);j++){          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           k=k+1;        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
           gm[k]=pmmij[i][j];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         }  
       }  
              /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        oldm=newm;
       for(theta=1; theta <=npar; theta++)      }
       trgradg[j][theta]=gradg[theta][j];      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          po[i][j][h]=newm[i][j];
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
      pmij(pmmij,cov,ncovmodel,x,nlstate);      /*printf("h=%d ",h);*/
     } /* end h */
      k=0;  /*     printf("\n H=%d \n",h); */
      for(i=1; i<=(nlstate+ndeath); i++){    return po;
        for(j=1; j<=(nlstate+ndeath);j++){  }
          k=k+1;  
          gm[k]=pmmij[i][j];  #ifdef NLOPT
         }    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
      }    double fret;
          double *xt;
      /*printf("\n%d ",(int)age);    int j;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    myfunc_data *d2 = (myfunc_data *) pd;
          /* xt = (p1-1); */
     xt=vector(1,n); 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
      }*/  
     fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
   fprintf(ficresprob,"\n%d ",(int)age);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     printf("Function = %.12lf ",fret);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    printf("\n");
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);   free_vector(xt,1,n);
   }    return fret;
   }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  #endif
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  /*************** log-likelihood *************/
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  double func( double *x)
 }  {
  free_vector(xp,1,npar);    int i, ii, j, k, mi, d, kk;
 fclose(ficresprob);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
  exit(0);    double **out;
 }    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 /***********************************************/    int s1, s2;
 /**************** Main Program *****************/    double bbh, survp;
 /***********************************************/    long ipmx;
     /*extern weight */
 /*int main(int argc, char *argv[])*/    /* We are differentiating ll according to initial status */
 int main()    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 {    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    */
   double agedeb, agefin,hf;  
   double agemin=1.e20, agemax=-1.e20;    ++countcallfunc;
   
   double fret;    cov[1]=1.;
   double **xi,tmp,delta;  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   double dum; /* Dummy variable */  
   double ***p3mat;    if(mle==1){
   int *indx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   char line[MAXLINE], linepar[MAXLINE];        /* Computes the values of the ncovmodel covariates of the model
   char title[MAXLINE];           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];           to be observed in j being in i according to the model.
   char filerest[FILENAMELENGTH];         */
   char fileregp[FILENAMELENGTH];        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   char popfile[FILENAMELENGTH];          cov[2+k]=covar[Tvar[k]][i];
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        }
   int firstobs=1, lastobs=10;        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   int sdeb, sfin; /* Status at beginning and end */           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   int c,  h , cpt,l;           has been calculated etc */
   int ju,jl, mi;        for(mi=1; mi<= wav[i]-1; mi++){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            for (j=1;j<=nlstate+ndeath;j++){
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int hstepm, nhstepm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int *popage;            }
           for(d=0; d<dh[mi][i]; d++){
   double bage, fage, age, agelim, agebase;            newm=savm;
   double ftolpl=FTOL;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **prlim;            for (kk=1; kk<=cptcovage;kk++) {
   double *severity;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
   double ***param; /* Matrix of parameters */            }
   double  *p;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double **matcov; /* Matrix of covariance */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***delti3; /* Scale */            savm=oldm;
   double *delti; /* Scale */            oldm=newm;
   double ***eij, ***vareij;          } /* end mult */
   double **varpl; /* Variances of prevalence limits by age */        
   double *epj, vepp;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double kk1, kk2;          /* But now since version 0.9 we anticipate for bias at large stepm.
   double *popeffectif,*popcount;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";           * the nearest (and in case of equal distance, to the lowest) interval but now
   char *alph[]={"a","a","b","c","d","e"}, str[4];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
   char z[1]="c", occ;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 #include <sys/time.h>           * -stepm/2 to stepm/2 .
 #include <time.h>           * For stepm=1 the results are the same as for previous versions of Imach.
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];           * For stepm > 1 the results are less biased than in previous versions. 
   /* long total_usecs;           */
   struct timeval start_time, end_time;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   printf("\nIMACH, Version 0.7");           */
   printf("\nEnter the parameter file name: ");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
 #ifdef windows            /* i.e. if s2 is a death state and if the date of death is known 
   scanf("%s",pathtot);               then the contribution to the likelihood is the probability to 
   getcwd(pathcd, size);               die between last step unit time and current  step unit time, 
   /*cygwin_split_path(pathtot,path,optionfile);               which is also equal to probability to die before dh 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/               minus probability to die before dh-stepm . 
   /* cutv(path,optionfile,pathtot,'\\');*/               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
 split(pathtot, path,optionfile);          health state: the date of the interview describes the actual state
   chdir(path);          and not the date of a change in health state. The former idea was
   replace(pathc,path);          to consider that at each interview the state was recorded
 #endif          (healthy, disable or death) and IMaCh was corrected; but when we
 #ifdef unix          introduced the exact date of death then we should have modified
   scanf("%s",optionfile);          the contribution of an exact death to the likelihood. This new
 #endif          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
 /*-------- arguments in the command line --------*/          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
   strcpy(fileres,"r");          probability to die within a month. Thanks to Chris
   strcat(fileres, optionfile);          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
   /*---------arguments file --------*/          which slows down the processing. The difference can be up to 10%
           lower mortality.
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            */
     printf("Problem with optionfile %s\n",optionfile);            lli=log(out[s1][s2] - savm[s1][s2]);
     goto end;  
   }  
           } else if  (s2==-2) {
   strcpy(filereso,"o");            for (j=1,survp=0. ; j<=nlstate; j++) 
   strcat(filereso,fileres);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   if((ficparo=fopen(filereso,"w"))==NULL) {            /*survp += out[s1][j]; */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            lli= log(survp);
   }          }
           
   /* Reads comments: lines beginning with '#' */          else if  (s2==-4) { 
   while((c=getc(ficpar))=='#' && c!= EOF){            for (j=3,survp=0. ; j<=nlstate; j++)  
     ungetc(c,ficpar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     fgets(line, MAXLINE, ficpar);            lli= log(survp); 
     puts(line);          } 
     fputs(line,ficparo);  
   }          else if  (s2==-5) { 
   ungetc(c,ficpar);            for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);            lli= log(survp); 
   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);          } 
   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);          
 while((c=getc(ficpar))=='#' && c!= EOF){          else{
     ungetc(c,ficpar);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     fgets(line, MAXLINE, ficpar);            /*  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 */
     puts(line);          } 
     fputs(line,ficparo);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   }          /*if(lli ==000.0)*/
   ungetc(c,ficpar);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            ipmx +=1;
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);          sw += weight[i];
   fprintf(ficparo,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
  while((c=getc(ficpar))=='#' && c!= EOF){      } /* end of individual */
     ungetc(c,ficpar);    }  else if(mle==2){
     fgets(line, MAXLINE, ficpar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     puts(line);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fputs(line,ficparo);        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   ungetc(c,ficpar);            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficparo,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);            }
                for(d=0; d<=dh[mi][i]; d++){
              newm=savm;
 while((c=getc(ficpar))=='#' && c!= EOF){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     ungetc(c,ficpar);            for (kk=1; kk<=cptcovage;kk++) {
     fgets(line, MAXLINE, ficpar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     puts(line);            }
     fputs(line,ficparo);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   ungetc(c,ficpar);            savm=oldm;
              oldm=newm;
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);          } /* end mult */
          
   covar=matrix(0,NCOVMAX,1,n);          s1=s[mw[mi][i]][i];
   cptcovn=0;          s2=s[mw[mi+1][i]][i];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          bbh=(double)bh[mi][i]/(double)stepm; 
           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 */
   ncovmodel=2+cptcovn;          ipmx +=1;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Read guess parameters */        } /* end of wave */
   /* Reads comments: lines beginning with '#' */      } /* end of individual */
   while((c=getc(ficpar))=='#' && c!= EOF){    }  else if(mle==3){  /* exponential inter-extrapolation */
     ungetc(c,ficpar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fgets(line, MAXLINE, ficpar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     puts(line);        for(mi=1; mi<= wav[i]-1; mi++){
     fputs(line,ficparo);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   ungetc(c,ficpar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            }
     for(i=1; i <=nlstate; i++)          for(d=0; d<dh[mi][i]; d++){
     for(j=1; j <=nlstate+ndeath-1; j++){            newm=savm;
       fscanf(ficpar,"%1d%1d",&i1,&j1);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       fprintf(ficparo,"%1d%1d",i1,j1);            for (kk=1; kk<=cptcovage;kk++) {
       printf("%1d%1d",i,j);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(k=1; k<=ncovmodel;k++){            }
         fscanf(ficpar," %lf",&param[i][j][k]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         printf(" %lf",param[i][j][k]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         fprintf(ficparo," %lf",param[i][j][k]);            savm=oldm;
       }            oldm=newm;
       fscanf(ficpar,"\n");          } /* end mult */
       printf("\n");        
       fprintf(ficparo,"\n");          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          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;
   p=param[1][1];          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Reads comments: lines beginning with '#' */        } /* end of wave */
   while((c=getc(ficpar))=='#' && c!= EOF){      } /* end of individual */
     ungetc(c,ficpar);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     fgets(line, MAXLINE, ficpar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     puts(line);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fputs(line,ficparo);        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   ungetc(c,ficpar);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            }
   for(i=1; i <=nlstate; i++){          for(d=0; d<dh[mi][i]; d++){
     for(j=1; j <=nlstate+ndeath-1; j++){            newm=savm;
       fscanf(ficpar,"%1d%1d",&i1,&j1);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       printf("%1d%1d",i,j);            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficparo,"%1d%1d",i1,j1);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(k=1; k<=ncovmodel;k++){            }
         fscanf(ficpar,"%le",&delti3[i][j][k]);          
         printf(" %le",delti3[i][j][k]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         fprintf(ficparo," %le",delti3[i][j][k]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       fscanf(ficpar,"\n");            oldm=newm;
       printf("\n");          } /* end mult */
       fprintf(ficparo,"\n");        
     }          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   delti=delti3[1][1];          if( s2 > nlstate){ 
              lli=log(out[s1][s2] - savm[s1][s2]);
   /* Reads comments: lines beginning with '#' */          }else{
   while((c=getc(ficpar))=='#' && c!= EOF){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          ipmx +=1;
     puts(line);          sw += weight[i];
     fputs(line,ficparo);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   ungetc(c,ficpar);        } /* end of wave */
        } /* end of individual */
   matcov=matrix(1,npar,1,npar);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   for(i=1; i <=npar; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fscanf(ficpar,"%s",&str);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf("%s",str);        for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficparo,"%s",str);          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=1; j <=i; j++){            for (j=1;j<=nlstate+ndeath;j++){
       fscanf(ficpar," %le",&matcov[i][j]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf(" %.5le",matcov[i][j]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficparo," %.5le",matcov[i][j]);            }
     }          for(d=0; d<dh[mi][i]; d++){
     fscanf(ficpar,"\n");            newm=savm;
     printf("\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fprintf(ficparo,"\n");            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i <=npar; i++)            }
     for(j=i+1;j<=npar;j++)          
       matcov[i][j]=matcov[j][i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("\n");            savm=oldm;
             oldm=newm;
           } /* end mult */
     /*-------- data file ----------*/        
     if((ficres =fopen(fileres,"w"))==NULL) {          s1=s[mw[mi][i]][i];
       printf("Problem with resultfile: %s\n", fileres);goto end;          s2=s[mw[mi+1][i]][i];
     }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     fprintf(ficres,"#%s\n",version);          ipmx +=1;
              sw += weight[i];
     if((fic=fopen(datafile,"r"))==NULL)    {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       printf("Problem with datafile: %s\n", datafile);goto end;          /*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 */
     n= lastobs;    } /* End of if */
     severity = vector(1,maxwav);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     outcome=imatrix(1,maxwav+1,1,n);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     num=ivector(1,n);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     moisnais=vector(1,n);    return -l;
     annais=vector(1,n);  }
     moisdc=vector(1,n);  
     andc=vector(1,n);  /*************** log-likelihood *************/
     agedc=vector(1,n);  double funcone( double *x)
     cod=ivector(1,n);  {
     weight=vector(1,n);    /* Same as likeli but slower because of a lot of printf and if */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    int i, ii, j, k, mi, d, kk;
     mint=matrix(1,maxwav,1,n);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     anint=matrix(1,maxwav,1,n);    double **out;
     s=imatrix(1,maxwav+1,1,n);    double lli; /* Individual log likelihood */
     adl=imatrix(1,maxwav+1,1,n);        double llt;
     tab=ivector(1,NCOVMAX);    int s1, s2;
     ncodemax=ivector(1,8);    double bbh, survp;
     /*extern weight */
     i=1;    /* We are differentiating ll according to initial status */
     while (fgets(line, MAXLINE, fic) != NULL)    {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       if ((i >= firstobs) && (i <=lastobs)) {    /*for(i=1;i<imx;i++) 
              printf(" %d\n",s[4][i]);
         for (j=maxwav;j>=1;j--){    */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    cov[1]=1.;
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for(k=1; k<=nlstate; k++) ll[k]=0.;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
              for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      for(mi=1; mi<= wav[i]-1; mi++){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        for(d=0; d<dh[mi][i]; d++){
         for (j=ncov;j>=1;j--){          newm=savm;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }          for (kk=1; kk<=cptcovage;kk++) {
         num[i]=atol(stra);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                  }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         i=i+1;          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
       }          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
     }          savm=oldm;
     /* printf("ii=%d", ij);          oldm=newm;
        scanf("%d",i);*/        } /* end mult */
   imx=i-1; /* Number of individuals */        
         s1=s[mw[mi][i]][i];
   /* for (i=1; i<=imx; i++){        s2=s[mw[mi+1][i]][i];
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        bbh=(double)bh[mi][i]/(double)stepm; 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        /* bias is positive if real duration
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;         * is higher than the multiple of stepm and negative otherwise.
     }         */
     for (i=1; i<=imx; i++) 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]));*/        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
   /* Calculation of the number of parameter from char model*/        } else if  (s2==-2) {
   Tvar=ivector(1,15);          for (j=1,survp=0. ; j<=nlstate; j++) 
   Tprod=ivector(1,15);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   Tvaraff=ivector(1,15);          lli= log(survp);
   Tvard=imatrix(1,15,1,2);        }else if (mle==1){
   Tage=ivector(1,15);                lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
            } else if(mle==2){
   if (strlen(model) >1){          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 */
     j=0, j1=0, k1=1, k2=1;        } else if(mle==3){  /* exponential inter-extrapolation */
     j=nbocc(model,'+');          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 */
     j1=nbocc(model,'*');        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     cptcovn=j+1;          lli=log(out[s1][s2]); /* Original formula */
     cptcovprod=j1;        } else{  /* mle=0 back to 1 */
              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
              /*lli=log(out[s1][s2]); */ /* Original formula */
     strcpy(modelsav,model);        } /* End of if */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        ipmx +=1;
       printf("Error. Non available option model=%s ",model);        sw += weight[i];
       goto end;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
            if(globpr){
     for(i=(j+1); i>=1;i--){          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       cutv(stra,strb,modelsav,'+');   %11.6f %11.6f %11.6f ", \
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       /*scanf("%d",i);*/          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       if (strchr(strb,'*')) {            llt +=ll[k]*gipmx/gsw;
         cutv(strd,strc,strb,'*');            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         if (strcmp(strc,"age")==0) {          }
           cptcovprod--;          fprintf(ficresilk," %10.6f\n", -llt);
           cutv(strb,stre,strd,'V');        }
           Tvar[i]=atoi(stre);      } /* end of wave */
           cptcovage++;    } /* end of individual */
             Tage[cptcovage]=i;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             /*printf("stre=%s ", stre);*/    /* 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 */
         else if (strcmp(strd,"age")==0) {    if(globpr==0){ /* First time we count the contributions and weights */
           cptcovprod--;      gipmx=ipmx;
           cutv(strb,stre,strc,'V');      gsw=sw;
           Tvar[i]=atoi(stre);    }
           cptcovage++;    return -l;
           Tage[cptcovage]=i;  }
         }  
         else {  
           cutv(strb,stre,strc,'V');  /*************** function likelione ***********/
           Tvar[i]=ncov+k1;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
           cutv(strb,strc,strd,'V');  {
           Tprod[k1]=i;    /* This routine should help understanding what is done with 
           Tvard[k1][1]=atoi(strc);       the selection of individuals/waves and
           Tvard[k1][2]=atoi(stre);       to check the exact contribution to the likelihood.
           Tvar[cptcovn+k2]=Tvard[k1][1];       Plotting could be done.
           Tvar[cptcovn+k2+1]=Tvard[k1][2];     */
           for (k=1; k<=lastobs;k++)    int k;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;    if(*globpri !=0){ /* Just counts and sums, no printings */
           k2=k2+2;      strcpy(fileresilk,"ilk"); 
         }      strcat(fileresilk,fileres);
       }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       else {        printf("Problem with resultfile: %s\n", fileresilk);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
        /*  scanf("%d",i);*/      }
       cutv(strd,strc,strb,'V');      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");
       Tvar[i]=atoi(strc);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       }      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       strcpy(modelsav,stra);        for(k=1; k<=nlstate; k++) 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         scanf("%d",i);*/      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }    }
 }  
      *fretone=(*funcone)(p);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    if(*globpri !=0){
   printf("cptcovprod=%d ", cptcovprod);      fclose(ficresilk);
   scanf("%d ",i);*/      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     fclose(fic);      fflush(fichtm); 
     } 
     /*  if(mle==1){*/    return;
     if (weightopt != 1) { /* Maximisation without weights*/  }
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }  
     /*-calculation of age at interview from date of interview and age at death -*/  /*********** Maximum Likelihood Estimation ***************/
     agev=matrix(1,maxwav,1,imx);  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    for (i=1; i<=imx; i++)  {
      for(m=2; (m<= maxwav); m++)    int i,j, iter=0;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    double **xi;
          anint[m][i]=9999;    double fret;
          s[m][i]=-1;    double fretone; /* Only one call to likelihood */
        }    /*  char filerespow[FILENAMELENGTH];*/
      
     for (i=1; i<=imx; i++)  {  #ifdef NLOPT
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    int creturn;
       for(m=1; (m<= maxwav); m++){    nlopt_opt opt;
         if(s[m][i] >0){    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
           if (s[m][i] == nlstate+1) {    double *lb;
             if(agedc[i]>0)    double minf; /* the minimum objective value, upon return */
               if(moisdc[i]!=99 && andc[i]!=9999)    double * p1; /* Shifted parameters from 0 instead of 1 */
               agev[m][i]=agedc[i];    myfunc_data dinst, *d = &dinst;
             else {  #endif
               if (andc[i]!=9999){  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    xi=matrix(1,npar,1,npar);
               }    for (i=1;i<=npar;i++)
             }      for (j=1;j<=npar;j++)
           }        xi[i][j]=(i==j ? 1.0 : 0.0);
           else if(s[m][i] !=9){ /* Should no more exist */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    strcpy(filerespow,"pow"); 
             if(mint[m][i]==99 || anint[m][i]==9999)    strcat(filerespow,fileres);
               agev[m][i]=1;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
             else if(agev[m][i] <agemin){      printf("Problem with resultfile: %s\n", filerespow);
               agemin=agev[m][i];      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    }
             }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
             else if(agev[m][i] >agemax){    for (i=1;i<=nlstate;i++)
               agemax=agev[m][i];      for(j=1;j<=nlstate+ndeath;j++)
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
             }    fprintf(ficrespow,"\n");
             /*agev[m][i]=anint[m][i]-annais[i];*/  #ifdef POWELL
             /*   agev[m][i] = age[i]+2*m;*/    powell(p,xi,npar,ftol,&iter,&fret,func);
           }  #endif
           else { /* =9 */  
             agev[m][i]=1;  #ifdef NLOPT
             s[m][i]=-1;  #ifdef NEWUOA
           }    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
         }  #else
         else /*= 0 Unknown */    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
           agev[m][i]=1;  #endif
       }    lb=vector(0,npar-1);
        for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     }    nlopt_set_lower_bounds(opt, lb);
     for (i=1; i<=imx; i++)  {    nlopt_set_initial_step1(opt, 0.1);
       for(m=1; (m<= maxwav); m++){    
         if (s[m][i] > (nlstate+ndeath)) {    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
           printf("Error: Wrong value in nlstate or ndeath\n");      d->function = func;
           goto end;    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
         }    nlopt_set_min_objective(opt, myfunc, d);
       }    nlopt_set_xtol_rel(opt, ftol);
     }    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    }
     else {
     free_vector(severity,1,maxwav);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
     free_imatrix(outcome,1,maxwav+1,1,n);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
     free_vector(moisnais,1,n);      iter=1; /* not equal */
     free_vector(annais,1,n);    }
     /* free_matrix(mint,1,maxwav,1,n);    nlopt_destroy(opt);
        free_matrix(anint,1,maxwav,1,n);*/  #endif
     free_vector(moisdc,1,n);    free_matrix(xi,1,npar,1,npar);
     free_vector(andc,1,n);    fclose(ficrespow);
     printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
        fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     wav=ivector(1,imx);    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  }
      
     /* Concatenates waves */  /**** Computes Hessian and covariance matrix ***/
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
     double  **a,**y,*x,pd;
       Tcode=ivector(1,100);    double **hess;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    int i, j;
       ncodemax[1]=1;    int *indx;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
          double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
    codtab=imatrix(1,100,1,10);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
    h=0;    void lubksb(double **a, int npar, int *indx, double b[]) ;
    m=pow(2,cptcoveff);    void ludcmp(double **a, int npar, int *indx, double *d) ;
      double gompertz(double p[]);
    for(k=1;k<=cptcoveff; k++){    hess=matrix(1,npar,1,npar);
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){    printf("\nCalculation of the hessian matrix. Wait...\n");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
            h++;    for (i=1;i<=npar;i++){
            if (h>m) h=1;codtab[h][k]=j;      printf("%d",i);fflush(stdout);
          }      fprintf(ficlog,"%d",i);fflush(ficlog);
        }     
      }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
    }      
          /*  printf(" %f ",p[i]);
    /* Calculates basic frequencies. Computes observed prevalence at single age          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
        and prints on file fileres'p'. */    }
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint);    
      for (i=1;i<=npar;i++) {
   free_matrix(mint,1,maxwav,1,n);      for (j=1;j<=npar;j++)  {
   free_matrix(anint,1,maxwav,1,n);        if (j>i) { 
            printf(".%d%d",i,j);fflush(stdout);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          hess[i][j]=hessij(p,delti,i,j,func,npar);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          hess[j][i]=hess[i][j];    
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          /*printf(" %lf ",hess[i][j]);*/
              }
     /* 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) */    printf("\n");
     fprintf(ficlog,"\n");
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
        
     /*--------- results files --------------*/    a=matrix(1,npar,1,npar);
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    y=matrix(1,npar,1,npar);
    fprintf(ficres,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);    x=vector(1,npar);
    fprintf(ficres,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
    jk=1;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
    fprintf(ficres,"# Parameters\n");    ludcmp(a,npar,indx,&pd);
    printf("# Parameters\n");  
    for(i=1,jk=1; i <=nlstate; i++){    for (j=1;j<=npar;j++) {
      for(k=1; k <=(nlstate+ndeath); k++){      for (i=1;i<=npar;i++) x[i]=0;
        if (k != i)      x[j]=1;
          {      lubksb(a,npar,indx,x);
            printf("%d%d ",i,k);      for (i=1;i<=npar;i++){ 
            fprintf(ficres,"%1d%1d ",i,k);        matcov[i][j]=x[i];
            for(j=1; j <=ncovmodel; j++){      }
              printf("%f ",p[jk]);    }
              fprintf(ficres,"%f ",p[jk]);  
              jk++;    printf("\n#Hessian matrix#\n");
            }    fprintf(ficlog,"\n#Hessian matrix#\n");
            printf("\n");    for (i=1;i<=npar;i++) { 
            fprintf(ficres,"\n");      for (j=1;j<=npar;j++) { 
          }        printf("%.3e ",hess[i][j]);
      }        fprintf(ficlog,"%.3e ",hess[i][j]);
    }      }
  if(mle==1){      printf("\n");
     /* Computing hessian and covariance matrix */      fprintf(ficlog,"\n");
     ftolhess=ftol; /* Usually correct */    }
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }    /* Recompute Inverse */
     fprintf(ficres,"# Scales\n");    for (i=1;i<=npar;i++)
     printf("# Scales\n");      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      for(i=1,jk=1; i <=nlstate; i++){    ludcmp(a,npar,indx,&pd);
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {    /*  printf("\n#Hessian matrix recomputed#\n");
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);    for (j=1;j<=npar;j++) {
           for(k=1; k<=ncovmodel;k++){      for (i=1;i<=npar;i++) x[i]=0;
             printf(" %.5e",delti[jk]);      x[j]=1;
             fprintf(ficres," %.5e",delti[jk]);      lubksb(a,npar,indx,x);
             jk++;      for (i=1;i<=npar;i++){ 
           }        y[i][j]=x[i];
           printf("\n");        printf("%.3e ",y[i][j]);
           fprintf(ficres,"\n");        fprintf(ficlog,"%.3e ",y[i][j]);
         }      }
       }      printf("\n");
       }      fprintf(ficlog,"\n");
        }
     k=1;    */
     fprintf(ficres,"# Covariance\n");  
     printf("# Covariance\n");    free_matrix(a,1,npar,1,npar);
     for(i=1;i<=npar;i++){    free_matrix(y,1,npar,1,npar);
       /*  if (k>nlstate) k=1;    free_vector(x,1,npar);
       i1=(i-1)/(ncovmodel*nlstate)+1;    free_ivector(indx,1,npar);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    free_matrix(hess,1,npar,1,npar);
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);  }
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);  /*************** hessian matrix ****************/
         printf(" %.5e",matcov[i][j]);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       }  {
       fprintf(ficres,"\n");    int i;
       printf("\n");    int l=1, lmax=20;
       k++;    double k1,k2;
     }    double p2[MAXPARM+1]; /* identical to x */
        double res;
     while((c=getc(ficpar))=='#' && c!= EOF){    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       ungetc(c,ficpar);    double fx;
       fgets(line, MAXLINE, ficpar);    int k=0,kmax=10;
       puts(line);    double l1;
       fputs(line,ficparo);  
     }    fx=func(x);
     ungetc(c,ficpar);    for (i=1;i<=npar;i++) p2[i]=x[i];
      for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      l1=pow(10,l);
          delts=delt;
     if (fage <= 2) {      for(k=1 ; k <kmax; k=k+1){
       bage = agemin;        delt = delta*(l1*k);
       fage = agemax;        p2[theta]=x[theta] +delt;
     }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         p2[theta]=x[theta]-delt;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        k2=func(p2)-fx;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
            
 /*------------ gnuplot -------------*/  #ifdef DEBUGHESS
 chdir(pathcd);        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);
   if((ficgp=fopen("graph.plt","w"))==NULL) {        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     printf("Problem with file graph.gp");goto end;  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 #ifdef windows        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   fprintf(ficgp,"cd \"%s\" \n",pathc);          k=kmax;
 #endif        }
 m=pow(2,cptcoveff);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
            k=kmax; l=lmax*10;
  /* 1eme*/        }
   for (cpt=1; cpt<= nlstate ; cpt ++) {        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
    for (k1=1; k1<= m ; k1 ++) {          delts=delt;
         }
 #ifdef windows      }
     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);    }
 #endif    delti[theta]=delts;
 #ifdef unix    return res; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    
 #endif  }
   
 for (i=1; i<= nlstate ; i ++) {  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  {
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int i;
 }    int l=1, lmax=20;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    double k1,k2,k3,k4,res,fx;
     for (i=1; i<= nlstate ; i ++) {    double p2[MAXPARM+1];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int k;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    fx=func(x);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    for (k=1; k<=2; k++) {
      for (i=1; i<= nlstate ; i ++) {      for (i=1;i<=npar;i++) p2[i]=x[i];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      p2[thetai]=x[thetai]+delti[thetai]/k;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 }        k1=func(p2)-fx;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    
 #ifdef unix      p2[thetai]=x[thetai]+delti[thetai]/k;
 fprintf(ficgp,"\nset ter gif small size 400,300");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 #endif      k2=func(p2)-fx;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    
    }      p2[thetai]=x[thetai]-delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   /*2 eme*/      k3=func(p2)-fx;
     
   for (k1=1; k1<= m ; k1 ++) {      p2[thetai]=x[thetai]-delti[thetai]/k;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          k4=func(p2)-fx;
     for (i=1; i<= nlstate+1 ; i ++) {      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       k=2*i;  #ifdef DEBUG
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for (j=1; j<= nlstate+1 ; j ++) {      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);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  #endif
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      return res;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  /************** Inverse of matrix **************/
       for (j=1; j<= nlstate+1 ; j ++) {  void ludcmp(double **a, int n, int *indx, double *d) 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  { 
         else fprintf(ficgp," \%%*lf (\%%*lf)");    int i,imax,j,k; 
 }      double big,dum,sum,temp; 
       fprintf(ficgp,"\" t\"\" w l 0,");    double *vv; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);   
       for (j=1; j<= nlstate+1 ; j ++) {    vv=vector(1,n); 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    *d=1.0; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (i=1;i<=n;i++) { 
 }        big=0.0; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      for (j=1;j<=n;j++) 
       else fprintf(ficgp,"\" t\"\" w l 0,");        if ((temp=fabs(a[i][j])) > big) big=temp; 
     }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      vv[i]=1.0/big; 
   }    } 
      for (j=1;j<=n;j++) { 
   /*3eme*/      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
   for (k1=1; k1<= m ; k1 ++) {        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     for (cpt=1; cpt<= nlstate ; cpt ++) {        a[i][j]=sum; 
       k=2+nlstate*(cpt-1);      } 
       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);      big=0.0; 
       for (i=1; i< nlstate ; i ++) {      for (i=j;i<=n;i++) { 
         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);        sum=a[i][j]; 
       }        for (k=1;k<j;k++) 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          sum -= a[i][k]*a[k][j]; 
     }        a[i][j]=sum; 
   }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
            big=dum; 
   /* CV preval stat */          imax=i; 
   for (k1=1; k1<= m ; k1 ++) {        } 
     for (cpt=1; cpt<nlstate ; cpt ++) {      } 
       k=3;      if (j != imax) { 
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);        for (k=1;k<=n;k++) { 
       for (i=1; i< nlstate ; i ++)          dum=a[imax][k]; 
         fprintf(ficgp,"+$%d",k+i+1);          a[imax][k]=a[j][k]; 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          a[j][k]=dum; 
              } 
       l=3+(nlstate+ndeath)*cpt;        *d = -(*d); 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        vv[imax]=vv[j]; 
       for (i=1; i< nlstate ; i ++) {      } 
         l=3+(nlstate+ndeath)*cpt;      indx[j]=imax; 
         fprintf(ficgp,"+$%d",l+i+1);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       }      if (j != n) { 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          dum=1.0/(a[j][j]); 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
   }      } 
     free_vector(vv,1,n);  /* Doesn't work */
   /* proba elementaires */  ;
    for(i=1,jk=1; i <=nlstate; i++){  } 
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {  void lubksb(double **a, int n, int *indx, double b[]) 
         for(j=1; j <=ncovmodel; j++){  { 
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    int i,ii=0,ip,j; 
           /*fprintf(ficgp,"%s",alph[1]);*/    double sum; 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);   
           jk++;    for (i=1;i<=n;i++) { 
           fprintf(ficgp,"\n");      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; 
   for(jk=1; jk <=m; jk++) {      b[i]=sum; 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    } 
    i=1;    for (i=n;i>=1;i--) { 
    for(k2=1; k2<=nlstate; k2++) {      sum=b[i]; 
      k3=i;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
      for(k=1; k<=(nlstate+ndeath); k++) {      b[i]=sum/a[i][i]; 
        if (k != k2){    } 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  } 
 ij=1;  
         for(j=3; j <=ncovmodel; j++) {  void pstamp(FILE *fichier)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  {
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
             ij++;  }
           }  
           else  /************ Frequencies ********************/
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  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 */
           fprintf(ficgp,")/(1");    
            int i, m, jk, j1, bool, z1,j;
         for(k1=1; k1 <=nlstate; k1++){      int first;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    double ***freq; /* Frequencies */
 ij=1;    double *pp, **prop;
           for(j=3; j <=ncovmodel; j++){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    char fileresp[FILENAMELENGTH];
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    
             ij++;    pp=vector(1,nlstate);
           }    prop=matrix(1,nlstate,iagemin,iagemax+3);
           else    strcpy(fileresp,"p");
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    strcat(fileresp,fileres);
           }    if((ficresp=fopen(fileresp,"w"))==NULL) {
           fprintf(ficgp,")");      printf("Problem with prevalence resultfile: %s\n", fileresp);
         }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      exit(0);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    }
         i=i+ncovmodel;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
        }    j1=0;
      }    
    }    j=cptcoveff;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }  
        first=1;
   fclose(ficgp);  
        /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
 chdir(path);    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
        /*    j1++; */
     free_ivector(wav,1,imx);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            scanf("%d", i);*/
     free_ivector(num,1,n);        for (i=-5; i<=nlstate+ndeath; i++)  
     free_vector(agedc,1,n);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            for(m=iagemin; m <= iagemax+3; m++)
     fclose(ficparo);              freq[i][jk][m]=0;
     fclose(ficres);        
     /*  }*/        for (i=1; i<=nlstate; i++)  
              for(m=iagemin; m <= iagemax+3; m++)
    /*________fin mle=1_________*/            prop[i][m]=0;
            
         dateintsum=0;
          k2cpt=0;
     /* No more information from the sample is required now */        for (i=1; i<=imx; i++) {
   /* Reads comments: lines beginning with '#' */          bool=1;
   while((c=getc(ficpar))=='#' && c!= EOF){          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
     ungetc(c,ficpar);            for (z1=1; z1<=cptcoveff; z1++)       
     fgets(line, MAXLINE, ficpar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
     puts(line);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
     fputs(line,ficparo);                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", 
   ungetc(c,ficpar);                  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);*/
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              } 
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          }
 /*--------- index.htm --------*/   
           if (bool==1){
   strcpy(optionfilehtm,optionfile);            for(m=firstpass; m<=lastpass; m++){
   strcat(optionfilehtm,".htm");              k2=anint[m][i]+(mint[m][i]/12.);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     printf("Problem with %s \n",optionfilehtm);goto end;                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];
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">                if (m<lastpass) {
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 Total number of observations=%d <br>                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>                }
 <hr  size=\"2\" color=\"#EC5E5E\">                
 <li>Outputs files<br><br>\n                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                  dateintsum=dateintsum+k2;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>                  k2cpt++;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                /*}*/
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>            }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        } /* end i */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>         
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>        pstamp(ficresp);
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
  fprintf(fichtm," <li>Graphs</li><p>");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
  m=cptcoveff;          fprintf(ficlog, "\n#********** Variable "); 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficlog, "**********\n#");
  j1=0;        }
  for(k1=1; k1<=m;k1++){        for(i=1; i<=nlstate;i++) 
    for(i1=1; i1<=ncodemax[k1];i1++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        j1++;        fprintf(ficresp, "\n");
        if (cptcovn > 0) {        
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(i=iagemin; i <= iagemax+3; i++){
          for (cpt=1; cpt<=cptcoveff;cpt++)          if(i==iagemax+3){
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);            fprintf(ficlog,"Total");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          }else{
        }            if(first==1){
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>              first=0;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                  printf("See log file for details...\n");
        for(cpt=1; cpt<nlstate;cpt++){            }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            fprintf(ficlog,"Age %d", i);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          }
        }          for(jk=1; jk <=nlstate ; jk++){
     for(cpt=1; cpt<=nlstate;cpt++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              pp[jk] += freq[jk][m][i]; 
 interval) in state (%d): v%s%d%d.gif <br>          }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            for(jk=1; jk <=nlstate ; jk++){
      }            for(m=-1, pos=0; m <=0 ; m++)
      for(cpt=1; cpt<=nlstate;cpt++) {              pos += freq[jk][m][i];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            if(pp[jk]>=1.e-10){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              if(first==1){
      }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              }
 health expectancies in states (1) and (2): e%s%d.gif<br>              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            }else{
 fprintf(fichtm,"\n</body>");              if(first==1)
    }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 fclose(fichtm);            }
           }
   /*--------------- Prevalence limit --------------*/  
            for(jk=1; jk <=nlstate ; jk++){
   strcpy(filerespl,"pl");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   strcat(filerespl,fileres);              pp[jk] += freq[jk][m][i];
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          }       
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   }            pos += pp[jk];
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            posprop += prop[jk][i];
   fprintf(ficrespl,"#Prevalence limit\n");          }
   fprintf(ficrespl,"#Age ");          for(jk=1; jk <=nlstate ; jk++){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            if(pos>=1.e-5){
   fprintf(ficrespl,"\n");              if(first==1)
                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   prlim=matrix(1,nlstate,1,nlstate);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }else{
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if(first==1)
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            }
   k=0;            if( i <= iagemax){
   agebase=agemin;              if(pos>=1.e-5){
   agelim=agemax;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   ftolpl=1.e-10;                /*probs[i][jk][j1]= pp[jk]/pos;*/
   i1=cptcoveff;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   if (cptcovn < 1){i1=1;}              }
               else
   for(cptcov=1;cptcov<=i1;cptcov++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            }
         k=k+1;          }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          
         fprintf(ficrespl,"\n#******");          for(jk=-1; jk <=nlstate+ndeath; jk++)
         for(j=1;j<=cptcoveff;j++)            for(m=-1; m <=nlstate+ndeath; m++)
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              if(freq[jk][m][i] !=0 ) {
         fprintf(ficrespl,"******\n");              if(first==1)
                        printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         for (age=agebase; age<=agelim; age++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              }
           fprintf(ficrespl,"%.0f",age );          if(i <= iagemax)
           for(i=1; i<=nlstate;i++)            fprintf(ficresp,"\n");
           fprintf(ficrespl," %.5f", prlim[i][i]);          if(first==1)
           fprintf(ficrespl,"\n");            printf("Others in log...\n");
         }          fprintf(ficlog,"\n");
       }        }
     }        /*}*/
   fclose(ficrespl);    }
     dateintmean=dateintsum/k2cpt; 
   /*------------- h Pij x at various ages ------------*/   
      fclose(ficresp);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    free_vector(pp,1,nlstate);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   }    /* End of Freq */
   printf("Computing pij: result on file '%s' \n", filerespij);  }
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /************ Prevalence ********************/
   /*if (stepm<=24) stepsize=2;*/  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
   agelim=AGESUP;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   hstepm=stepsize*YEARM; /* Every year of age */       in each health status at the date of interview (if between dateprev1 and dateprev2).
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       We still use firstpass and lastpass as another selection.
      */
   k=0;   
   for(cptcov=1;cptcov<=i1;cptcov++){    int i, m, jk, j1, bool, z1,j;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    double **prop;
         fprintf(ficrespij,"\n#****** ");    double posprop; 
         for(j=1;j<=cptcoveff;j++)    double  y2; /* in fractional years */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int iagemin, iagemax;
         fprintf(ficrespij,"******\n");    int first; /** to stop verbosity which is redirected to log file */
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    iagemin= (int) agemin;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    iagemax= (int) agemax;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /*pp=vector(1,nlstate);*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           oldm=oldms;savm=savms;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      j1=0;
           fprintf(ficrespij,"# Age");    
           for(i=1; i<=nlstate;i++)    /*j=cptcoveff;*/
             for(j=1; j<=nlstate+ndeath;j++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
               fprintf(ficrespij," %1d-%1d",i,j);    
           fprintf(ficrespij,"\n");    first=1;
           for (h=0; h<=nhstepm; h++){    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      /*for(i1=1; i1<=ncodemax[k1];i1++){
             for(i=1; i<=nlstate;i++)        j1++;*/
               for(j=1; j<=nlstate+ndeath;j++)        
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        for (i=1; i<=nlstate; i++)  
             fprintf(ficrespij,"\n");          for(m=iagemin; m <= iagemax+3; m++)
           }            prop[i][m]=0.0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       
           fprintf(ficrespij,"\n");        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]]) 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                bool=0;
           } 
   fclose(ficrespij);          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   /*---------- Forecasting ------------------*/              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   strcpy(fileresf,"f");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   strcat(fileresf,fileres);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   if((ficresf=fopen(fileresf,"w"))==NULL) {                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); 
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;                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]]);*/
   printf("Computing forecasting: result on file '%s' \n", fileresf);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);                } 
               }
  free_matrix(agev,1,maxwav,1,imx);            } /* end selection of waves */
   /* Mobile average */          }
         }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   if (mobilav==1) {            posprop += prop[jk][i]; 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          } 
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)          
       for (i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){     
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            if( i <=  iagemax){ 
           mobaverage[(int)agedeb][i][cptcod]=0.;              if(posprop>=1.e-5){ 
                    probs[i][jk][j1]= prop[jk][i]/posprop;
     for (agedeb=bage+4; agedeb<=fage; agedeb++){              } else{
       for (i=1; i<=nlstate;i++){                if(first==1){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                  first=0;
           for (cpt=0;cpt<=4;cpt++){                  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]);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                }
           }              }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            } 
         }          }/* end jk */ 
       }        }/* end i */ 
     }        /*} *//* end i1 */
   }    } /* end j1 */
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   if (stepm<=12) stepsize=1;    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   agelim=AGESUP;  }  /* End of prevalence */
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */  /************* Waves Concatenation ***************/
    
   if (popforecast==1) {  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     if((ficpop=fopen(popfile,"r"))==NULL)    {  {
       printf("Problem with population file : %s\n",popfile);goto end;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     }       Death is a valid wave (if date is known).
     popage=ivector(0,AGESUP);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     popeffectif=vector(0,AGESUP);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     popcount=vector(0,AGESUP);       and mw[mi+1][i]. dh depends on stepm.
        */
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)    int i, mi, m;
       {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         i=i+1;       double sum=0., jmean=0.;*/
       }    int first;
     imx=i;    int j, k=0,jk, ju, jl;
      double sum=0.;
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    first=0;
   }    jmin=100000;
     jmax=-1;
   for(cptcov=1;cptcov<=i1;cptcov++){    jmean=0.;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for(i=1; i<=imx; i++){
       k=k+1;      mi=0;
       fprintf(ficresf,"\n#****** ");      m=firstpass;
       for(j=1;j<=cptcoveff;j++) {      while(s[m][i] <= nlstate){
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       }          mw[++mi][i]=m;
       fprintf(ficresf,"******\n");        if(m >=lastpass)
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");          break;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        else
       if (popforecast==1)  fprintf(ficresf," [Population]");          m++;
       }/* end while */
       for (agedeb=fage; agedeb>=bage; agedeb--){      if (s[m][i] > nlstate){
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);        mi++;     /* Death is another wave */
        if (mobilav==1) {        /* if(mi==0)  never been interviewed correctly before death */
         for(j=1; j<=nlstate;j++)           /* Only death is a correct wave */
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);        mw[mi][i]=m;
         }      }
         else {  
           for(j=1; j<=nlstate;j++)      wav[i]=mi;
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);      if(mi==0){
         }          nbwarn++;
         if(first==0){
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);          first=1;
       }        }
              if(first==1){
       for (cpt=1; cpt<=nforecast;cpt++) {          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         fprintf(ficresf,"\n");        }
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      } /* end mi==0 */
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    } /* End individuals */
         nhstepm = nhstepm/hstepm;  
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (stepm <=0)
         oldm=oldms;savm=savms;          dh[mi][i]=1;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          else{
                          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         for (h=0; h<=nhstepm; h++){            if (agedc[i] < 2*AGESUP) {
                      j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
          if (h*hstepm/YEARM*stepm==cpt)              if(j==0) j=1;  /* Survives at least one month after exam */
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);              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]);
          for(j=1; j<=nlstate+ndeath;j++) {                j=1; /* Temporary Dangerous patch */
            kk1=0.;kk2=0;                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
            for(i=1; i<=nlstate;i++) {                        fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
              if (mobilav==1)                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);
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];              }
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];              k=k+1;
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];              if (j >= jmax){
             }                jmax=j;
            if (h*hstepm/YEARM*stepm==cpt) {                ijmax=i;
              fprintf(ficresf," %.3f", kk1);              }
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);              if (j <= jmin){
            }                jmin=j;
           }                ijmin=i;
         }              }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              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{
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   if (popforecast==1) {  /*        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]); */
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);            k=k+1;
     free_vector(popcount,0,AGESUP);            if (j >= jmax) {
   }              jmax=j;
   free_imatrix(s,1,maxwav+1,1,n);              ijmax=i;
   free_vector(weight,1,n);            }
   fclose(ficresf);            else if (j <= jmin){
   /*---------- Health expectancies and variances ------------*/              jmin=j;
               ijmin=i;
   strcpy(filerest,"t");            }
   strcat(filerest,fileres);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   if((ficrest=fopen(filerest,"w"))==NULL) {            /*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]);*/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            if(j<0){
   }              nberr++;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);              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]);
             }
   strcpy(filerese,"e");            sum=sum+j;
   strcat(filerese,fileres);          }
   if((ficreseij=fopen(filerese,"w"))==NULL) {          jk= j/stepm;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          jl= j -jk*stepm;
   }          ju= j -(jk+1)*stepm;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
  strcpy(fileresv,"v");              dh[mi][i]=jk;
   strcat(fileresv,fileres);              bh[mi][i]=0;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            }else{ /* We want a negative bias in order to only have interpolation ie
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                    * to avoid the price of an extra matrix product in likelihood */
   }              dh[mi][i]=jk+1;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              bh[mi][i]=ju;
             }
   k=0;          }else{
   for(cptcov=1;cptcov<=i1;cptcov++){            if(jl <= -ju){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              dh[mi][i]=jk;
       k=k+1;              bh[mi][i]=jl;       /* bias is positive if real duration
       fprintf(ficrest,"\n#****** ");                                   * is higher than the multiple of stepm and negative otherwise.
       for(j=1;j<=cptcoveff;j++)                                   */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
       fprintf(ficrest,"******\n");            else{
               dh[mi][i]=jk+1;
       fprintf(ficreseij,"\n#****** ");              bh[mi][i]=ju;
       for(j=1;j<=cptcoveff;j++)            }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            if(dh[mi][i]==0){
       fprintf(ficreseij,"******\n");              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
       fprintf(ficresvij,"\n#****** ");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
       for(j=1;j<=cptcoveff;j++)            }
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          } /* end if mle */
       fprintf(ficresvij,"******\n");        }
       } /* end wave */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    }
       oldm=oldms;savm=savms;    jmean=sum/k;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, 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);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    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);
       oldm=oldms;savm=savms;   }
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
        /*********** Tricode ****************************/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  {
       fprintf(ficrest,"\n");    /**< 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 
       hf=1;     * Boring subroutine which should only output nbcode[Tvar[j]][k]
       if (stepm >= YEARM) hf=stepm/YEARM;     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       epj=vector(1,nlstate+1);     * nbcode[Tvar[j]][1]= 
       for(age=bage; age <=fage ;age++){    */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
           for(i=1; i<=nlstate;i++)    int modmaxcovj=0; /* Modality max of covariates j */
             prlim[i][i]=probs[(int)age][i][k];    int cptcode=0; /* Modality max of covariates j */
         }    int modmincovj=0; /* Modality min of covariates j */
          
         fprintf(ficrest," %.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    cptcoveff=0; 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {   
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    for (k=-1; k < maxncov; k++) Ndum[k]=0;
           }    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
           epj[nlstate+1] +=epj[j];  
         }    /* Loop on covariates without age and products */
         for(i=1, vepp=0.;i <=nlstate;i++)    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
           for(j=1;j <=nlstate;j++)      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
             vepp += vareij[i][j][(int)age];                                 modality of this covariate Vj*/ 
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
         for(j=1;j <=nlstate;j++){                                      * If product of Vn*Vm, still boolean *:
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));                                      * 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   */
         fprintf(ficrest,"\n");        /* 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 );
  fclose(ficreseij);          exit(1);
  fclose(ficresvij);        }else
   fclose(ficrest);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   fclose(ficpar);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   free_vector(epj,1,nlstate+1);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   /*  scanf("%d ",i); */        /* 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
   /*------- Variance limit prevalence------*/             female is 1, then modmaxcovj=1.*/
       }
 strcpy(fileresvpl,"vpl");      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   strcat(fileresvpl,fileres);      cptcode=modmaxcovj;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);     /*for (i=0; i<=cptcode; i++) {*/
     exit(0);      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 V%d %d\n", j, Tvar[j], Ndum[i]);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
  k=0;        }
  for(cptcov=1;cptcov<=i1;cptcov++){        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
      k=k+1;      } /* Ndum[-1] number of undefined modalities */
      fprintf(ficresvpl,"\n#****** ");  
      for(j=1;j<=cptcoveff;j++)      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
      fprintf(ficresvpl,"******\n");      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
               modmincovj=3; modmaxcovj = 7;
      varpl=matrix(1,nlstate,(int) bage, (int) fage);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
      oldm=oldms;savm=savms;         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         variables V1_1 and V1_2.
    }         nbcode[Tvar[j]][ij]=k;
  }         nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
   fclose(ficresvpl);         nbcode[Tvar[j]][3]=2;
       */
   /*---------- End : free ----------------*/      ij=1; /* ij is similar to i but can jumps over null modalities */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      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 */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          /*recode from 0 */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
              nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                         k is a modality. If we have model=V1+V1*sex 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            ij++;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          if (ij > ncodemax[j]) break; 
          }  /* end of loop on */
   free_matrix(matcov,1,npar,1,npar);      } /* end of loop on modality */ 
   free_vector(delti,1,npar);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
      
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     
   printf("End of Imach\n");    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */     /* 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 */ 
   /* 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);*/     Ndum[ij]++; 
   /*printf("Total time was %d uSec.\n", total_usecs);*/   } 
   /*------ End -----------*/  
    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) */
  end:     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
 #ifdef windows     if((Ndum[i]!=0) && (i<=ncovcol)){
  chdir(pathcd);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
 #endif       Tvaraff[ij]=i; /*For printing (unclear) */
         ij++;
  system("..\\gp37mgw\\wgnuplot graph.plt");     }else
          Tvaraff[ij]=0;
 #ifdef windows   }
   while (z[0] != 'q') {   ij--;
     chdir(pathcd);   cptcoveff=ij; /*Number of total covariates*/
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  
     scanf("%s",z);  }
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') {  
       chdir(path);  /*********** Health Expectancies ****************/
       system(optionfilehtm);  
     }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     else if (z[0] == 'q') exit(0);  
   }  {
 #endif    /* 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;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
   
   #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 */
   }
   
   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");
           }
         /*}*/
       }
   }
   
   
   /***********************************************/
   /**************** 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;
     getcwd(pathcd, size);
   
     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);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       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.1.17  
changed lines
  Added in v.1.181


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