Diff for /imach/src/imach.c between versions 1.32 and 1.186

version 1.32, 2002/03/11 14:17:15 version 1.186, 2015/04/23 12:01:52
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.186  2015/04/23 12:01:52  brouard
      Summary: V1*age is working now, version 0.98q1
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Some codes had been disabled in order to simplify and Vn*age was
   first survey ("cross") where individuals from different ages are    working in the optimization phase, ie, giving correct MLE parameters,
   interviewed on their health status or degree of disability (in the    but, as usual, outputs were not correct and program core dumped.
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.185  2015/03/11 13:26:42  brouard
   (if any) in individual health status.  Health expectancies are    Summary: Inclusion of compile and links command line for Intel Compiler
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.184  2015/03/11 11:52:39  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Summary: Back from Windows 8. Intel Compiler
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.183  2015/03/10 20:34:32  brouard
   conditional to be observed in state i at the first wave. Therefore    Summary: 0.98q0, trying with directest, mnbrak fixed
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    We use directest instead of original Powell test; probably no
   complex model than "constant and age", you should modify the program    incidence on the results, but better justifications;
   where the markup *Covariates have to be included here again* invites    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   you to do it.  More covariates you add, slower the    wrong results.
   convergence.  
     Revision 1.182  2015/02/12 08:19:57  brouard
   The advantage of this computer programme, compared to a simple    Summary: Trying to keep directest which seems simpler and more general
   multinomial logistic model, is clear when the delay between waves is not    Author: Nicolas Brouard
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.181  2015/02/11 23:22:24  brouard
   account using an interpolation or extrapolation.      Summary: Comments on Powell added
   
   hPijx is the probability to be observed in state i at age x+h    Author:
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.180  2015/02/11 17:33:45  brouard
   states. This elementary transition (by month or quarter trimester,    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.179  2015/01/04 09:57:06  brouard
   and the contribution of each individual to the likelihood is simply    Summary: back to OS/X
   hPijx.  
     Revision 1.178  2015/01/04 09:35:48  brouard
   Also this programme outputs the covariance matrix of the parameters but also    *** empty log message ***
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.177  2015/01/03 18:40:56  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Summary: Still testing ilc32 on OSX
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.176  2015/01/03 16:45:04  brouard
   from the European Union.    *** empty log message ***
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.175  2015/01/03 16:33:42  brouard
   can be accessed at http://euroreves.ined.fr/imach .    *** empty log message ***
   **********************************************************************/  
      Revision 1.174  2015/01/03 16:15:49  brouard
 #include <math.h>    Summary: Still in cross-compilation
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.173  2015/01/03 12:06:26  brouard
 #include <unistd.h>    Summary: trying to detect cross-compilation
   
 #define MAXLINE 256    Revision 1.172  2014/12/27 12:07:47  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.171  2014/12/23 13:26:59  brouard
 #define windows    Summary: Back from Visual C
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Still problem with utsname.h on Windows
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.170  2014/12/23 11:17:12  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: Cleaning some \%% back to %%
   
 #define NINTERVMAX 8    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.169  2014/12/22 23:08:31  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: 0.98p
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.168  2014/12/22 15:17:42  brouard
     Summary: update
   
 int erreur; /* Error number */    Revision 1.167  2014/12/22 13:50:56  brouard
 int nvar;    Summary: Testing uname and compiler version and if compiled 32 or 64
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Testing on Linux 64
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.166  2014/12/22 11:40:47  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    *** empty log message ***
 int popbased=0;  
     Revision 1.165  2014/12/16 11:20:36  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Summary: After compiling on Visual C
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    * imach.c (Module): Merging 1.61 to 1.162
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.164  2014/12/16 10:52:11  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    * imach.c (Module): Merging 1.61 to 1.162
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.163  2014/12/16 10:30:11  brouard
 FILE *ficgp,*ficresprob,*ficpop;    * imach.c (Module): Merging 1.61 to 1.162
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.162  2014/09/25 11:43:39  brouard
  FILE  *ficresvij;    Summary: temporary backup 0.99!
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.1  2014/09/16 11:06:58  brouard
   char fileresvpl[FILENAMELENGTH];    Summary: With some code (wrong) for nlopt
   
 #define NR_END 1    Author:
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
 #define NRANSI  
 #define ITMAX 200    Revision 1.160  2014/09/02 09:24:05  brouard
     *** empty log message ***
 #define TOL 2.0e-4  
     Revision 1.159  2014/09/01 10:34:10  brouard
 #define CGOLD 0.3819660    Summary: WIN32
 #define ZEPS 1.0e-10    Author: Brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.158  2014/08/27 17:11:51  brouard
 #define GOLD 1.618034    *** empty log message ***
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.157  2014/08/27 16:26:55  brouard
     Summary: Preparing windows Visual studio version
 static double maxarg1,maxarg2;    Author: Brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    In order to compile on Visual studio, time.h is now correct and time_t
      and tm struct should be used. difftime should be used but sometimes I
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    just make the differences in raw time format (time(&now).
 #define rint(a) floor(a+0.5)    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.156  2014/08/25 20:10:10  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    *** empty log message ***
   
 int imx;    Revision 1.155  2014/08/25 18:32:34  brouard
 int stepm;    Summary: New compile, minor changes
 /* Stepm, step in month: minimum step interpolation*/    Author: Brouard
   
 int m,nb;    Revision 1.154  2014/06/20 17:32:08  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Summary: Outputs now all graphs of convergence to period prevalence
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.153  2014/06/20 16:45:46  brouard
 double dateintmean=0;    Summary: If 3 live state, convergence to period prevalence on same graph
     Author: Brouard
 double *weight;  
 int **s; /* Status */    Revision 1.152  2014/06/18 17:54:09  brouard
 double *agedc, **covar, idx;    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.151  2014/06/18 16:43:30  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    *** empty log message ***
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.150  2014/06/18 16:42:35  brouard
 /**************** split *************************/    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Author: brouard
 {  
    char *s;                             /* pointer */    Revision 1.149  2014/06/18 15:51:14  brouard
    int  l1, l2;                         /* length counters */    Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.148  2014/06/17 17:38:48  brouard
 #ifdef windows    Summary: Nothing new
    s = strrchr( path, '\\' );           /* find last / */    Author: Brouard
 #else  
    s = strrchr( path, '/' );            /* find last / */    Just a new packaging for OS/X version 0.98nS
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.147  2014/06/16 10:33:11  brouard
 #if     defined(__bsd__)                /* get current working directory */    *** empty log message ***
       extern char       *getwd( );  
     Revision 1.146  2014/06/16 10:20:28  brouard
       if ( getwd( dirc ) == NULL ) {    Summary: Merge
 #else    Author: Brouard
       extern char       *getcwd( );  
     Merge, before building revised version.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.145  2014/06/10 21:23:15  brouard
          return( GLOCK_ERROR_GETCWD );    Summary: Debugging with valgrind
       }    Author: Nicolas Brouard
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Lot of changes in order to output the results with some covariates
       s++;                              /* after this, the filename */    After the Edimburgh REVES conference 2014, it seems mandatory to
       l2 = strlen( s );                 /* length of filename */    improve the code.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    No more memory valgrind error but a lot has to be done in order to
       strcpy( name, s );                /* save file name */    continue the work of splitting the code into subroutines.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Also, decodemodel has been improved. Tricode is still not
       dirc[l1-l2] = 0;                  /* add zero */    optimal. nbcode should be improved. Documentation has been added in
    }    the source code.
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.143  2014/01/26 09:45:38  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #endif    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.142  2014/01/26 03:57:36  brouard
    strcpy(ext,s);                       /* save extension */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    l1= strlen( name);  
    l2= strlen( s)+1;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.141  2014/01/26 02:42:01  brouard
    return( 0 );                         /* we're done */    * 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.
 /******************************************/  
     Revision 1.139  2010/06/14 07:50:17  brouard
 void replace(char *s, char*t)    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 {    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   int i;  
   int lg=20;    Revision 1.138  2010/04/30 18:19:40  brouard
   i=0;    *** empty log message ***
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.137  2010/04/29 18:11:38  brouard
     (s[i] = t[i]);    (Module): Checking covariates for more complex models
     if (t[i]== '\\') s[i]='/';    than V1+V2. A lot of change to be done. Unstable.
   }  
 }    Revision 1.136  2010/04/26 20:30:53  brouard
     (Module): merging some libgsl code. Fixing computation
 int nbocc(char *s, char occ)    of likelione (using inter/intrapolation if mle = 0) in order to
 {    get same likelihood as if mle=1.
   int i,j=0;    Some cleaning of code and comments added.
   int lg=20;  
   i=0;    Revision 1.135  2009/10/29 15:33:14  brouard
   lg=strlen(s);    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.134  2009/10/29 13:18:53  brouard
   }    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   return j;  
 }    Revision 1.133  2009/07/06 10:21:25  brouard
     just nforces
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.132  2009/07/06 08:22:05  brouard
   int i,lg,j,p=0;    Many tings
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.131  2009/06/20 16:22:47  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Some dimensions resccaled
   }  
     Revision 1.130  2009/05/26 06:44:34  brouard
   lg=strlen(t);    (Module): Max Covariate is now set to 20 instead of 8. A
   for(j=0; j<p; j++) {    lot of cleaning with variables initialized to 0. Trying to make
     (u[j] = t[j]);    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
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
    for(j=0; j<= lg; j++) {  
     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
 }  
     Revision 1.127  2006/04/28 18:11:50  brouard
 /********************** nrerror ********************/    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 void nrerror(char error_text[])    loop. Now we define nhstepma in the age loop.
 {    (Module): In order to speed up (in case of numerous covariates) we
   fprintf(stderr,"ERREUR ...\n");    compute health expectancies (without variances) in a first step
   fprintf(stderr,"%s\n",error_text);    and then all the health expectancies with variances or standard
   exit(1);    deviation (needs data from the Hessian matrices) which slows the
 }    computation.
 /*********************** vector *******************/    In the future we should be able to stop the program is only health
 double *vector(int nl, int nh)    expectancies and graph are needed without standard deviations.
 {  
   double *v;    Revision 1.126  2006/04/28 17:23:28  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    (Module): Yes the sum of survivors was wrong since
   if (!v) nrerror("allocation failure in vector");    imach-114 because nhstepm was no more computed in the age
   return v-nl+NR_END;    loop. Now we define nhstepma in the age loop.
 }    Version 0.98h
   
 /************************ free vector ******************/    Revision 1.125  2006/04/04 15:20:31  lievre
 void free_vector(double*v, int nl, int nh)    Errors in calculation of health expectancies. Age was not initialized.
 {    Forecasting file added.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
 /************************ivector *******************************/    The log-likelihood is printed in the log file
 int *ivector(long nl,long nh)  
 {    Revision 1.123  2006/03/20 10:52:43  brouard
   int *v;    * imach.c (Module): <title> changed, corresponds to .htm file
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    name. <head> headers where missing.
   if (!v) nrerror("allocation failure in ivector");  
   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,
     otherwise the weight is truncated).
 /******************free ivector **************************/    Modification of warning when the covariates values are not 0 or
 void free_ivector(int *v, long nl, long nh)    1.
 {    Version 0.98g
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 /******************* imatrix *******************************/    English (a comma might work with a correct LC_NUMERIC environment,
 int **imatrix(long nrl, long nrh, long ncl, long nch)    otherwise the weight is truncated).
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Modification of warning when the covariates values are not 0 or
 {    1.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Version 0.98g
   int **m;  
      Revision 1.121  2006/03/16 17:45:01  lievre
   /* allocate pointers to rows */    * imach.c (Module): Comments concerning covariates added
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    * imach.c (Module): refinements in the computation of lli if
   m += NR_END;    status=-2 in order to have more reliable computation if stepm is
   m -= nrl;    not 1 month. Version 0.98f
    
      Revision 1.120  2006/03/16 15:10:38  lievre
   /* allocate rows and set pointers to them */    (Module): refinements in the computation of lli if
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    status=-2 in order to have more reliable computation if stepm is
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    not 1 month. Version 0.98f
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.119  2006/03/15 17:42:26  brouard
      (Module): Bug if status = -2, the loglikelihood was
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    computed as likelihood omitting the logarithm. Version O.98e
    
   /* return pointer to array of pointers to rows */    Revision 1.118  2006/03/14 18:20:07  brouard
   return m;    (Module): varevsij Comments added explaining the second
 }    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /****************** free_imatrix *************************/    (Module): Function pstamp added
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): Version 0.98d
       int **m;  
       long nch,ncl,nrh,nrl;    Revision 1.117  2006/03/14 17:16:22  brouard
      /* free an int matrix allocated by imatrix() */    (Module): varevsij Comments added explaining the second
 {    table of variances if popbased=1 .
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   free((FREE_ARG) (m+nrl-NR_END));    (Module): Function pstamp added
 }    (Module): Version 0.98d
   
 /******************* matrix *******************************/    Revision 1.116  2006/03/06 10:29:27  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    (Module): Variance-covariance wrong links and
 {    varian-covariance of ej. is needed (Saito).
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.114  2006/02/26 12:57:58  brouard
   m += NR_END;    (Module): Some improvements in processing parameter
   m -= nrl;    filename with strsep.
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.113  2006/02/24 14:20:24  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Memory leaks checks with valgrind and:
   m[nrl] += NR_END;    datafile was not closed, some imatrix were not freed and on matrix
   m[nrl] -= ncl;    allocation too.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.112  2006/01/30 09:55:26  brouard
   return m;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 }  
     Revision 1.111  2006/01/25 20:38:18  brouard
 /*************************free matrix ************************/    (Module): Lots of cleaning and bugs added (Gompertz)
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    (Module): Comments can be added in data file. Missing date values
 {    can be a simple dot '.'.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   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 *******************************/    Revision 1.109  2006/01/24 19:37:15  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    (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;    Revision 1.108  2006/01/19 18:05:42  lievre
   double ***m;    Gnuplot problem appeared...
     To be fixed
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.107  2006/01/19 16:20:37  brouard
   m += NR_END;    Test existence of gnuplot in imach path
   m -= nrl;  
     Revision 1.106  2006/01/19 13:24:36  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Some cleaning and links added in html output
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.105  2006/01/05 20:23:19  lievre
   m[nrl] -= ncl;    *** 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
     (Module): sump fixed, loop imx fixed, and simplifications.
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    (Module): If the status is missing at the last wave but we know
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    that the person is alive, then we can code his/her status as -2
   m[nrl][ncl] += NR_END;    (instead of missing=-1 in earlier versions) and his/her
   m[nrl][ncl] -= nll;    contributions to the likelihood is 1 - Prob of dying from last
   for (j=ncl+1; j<=nch; j++)    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     m[nrl][j]=m[nrl][j-1]+nlay;    the healthy state at last known wave). Version is 0.98
    
   for (i=nrl+1; i<=nrh; i++) {    Revision 1.103  2005/09/30 15:54:49  lievre
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    (Module): sump fixed, loop imx fixed, and simplifications.
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    Revision 1.102  2004/09/15 17:31:30  brouard
   }    Add the possibility to read data file including tab characters.
   return m;  
 }    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 /*************************free ma3x ************************/  
 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
 {    Add version for Mac OS X. Just define UNIX in Makefile
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.99  2004/06/05 08:57:40  brouard
   free((FREE_ARG)(m+nrl-NR_END));    *** empty log message ***
 }  
     Revision 1.98  2004/05/16 15:05:56  brouard
 /***************** f1dim *************************/    New version 0.97 . First attempt to estimate force of mortality
 extern int ncom;    directly from the data i.e. without the need of knowing the health
 extern double *pcom,*xicom;    state at each age, but using a Gompertz model: log u =a + b*age .
 extern double (*nrfunc)(double []);    This is the basic analysis of mortality and should be done before any
      other analysis, in order to test if the mortality estimated from the
 double f1dim(double x)    cross-longitudinal survey is different from the mortality estimated
 {    from other sources like vital statistic data.
   int j;  
   double f;    The same imach parameter file can be used but the option for mle should be -3.
   double *xt;  
      Agnès, who wrote this part of the code, tried to keep most of the
   xt=vector(1,ncom);    former routines in order to include the new code within the former code.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    The output is very simple: only an estimate of the intercept and of
   free_vector(xt,1,ncom);    the slope with 95% confident intervals.
   return f;  
 }    Current limitations:
     A) Even if you enter covariates, i.e. with the
 /*****************brent *************************/    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    B) There is no computation of Life Expectancy nor Life Table.
 {  
   int iter;    Revision 1.97  2004/02/20 13:25:42  lievre
   double a,b,d,etemp;    Version 0.96d. Population forecasting command line is (temporarily)
   double fu,fv,fw,fx;    suppressed.
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    Revision 1.96  2003/07/15 15:38:55  brouard
   double e=0.0;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
      rewritten within the same printf. Workaround: many printfs.
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    Revision 1.95  2003/07/08 07:54:34  brouard
   x=w=v=bx;    * imach.c (Repository):
   fw=fv=fx=(*f)(x);    (Repository): Using imachwizard code to output a more meaningful covariance
   for (iter=1;iter<=ITMAX;iter++) {    matrix (cov(a12,c31) instead of numbers.
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    Revision 1.94  2003/06/27 13:00:02  brouard
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    Just cleaning
     printf(".");fflush(stdout);  
 #ifdef DEBUG    Revision 1.93  2003/06/25 16:33:55  brouard
     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);    (Module): On windows (cygwin) function asctime_r doesn't
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    exist so I changed back to asctime which exists.
 #endif    (Module): Version 0.96b
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;    Revision 1.92  2003/06/25 16:30:45  brouard
       return fx;    (Module): On windows (cygwin) function asctime_r doesn't
     }    exist so I changed back to asctime which exists.
     ftemp=fu;  
     if (fabs(e) > tol1) {    Revision 1.91  2003/06/25 15:30:29  brouard
       r=(x-w)*(fx-fv);    * imach.c (Repository): Duplicated warning errors corrected.
       q=(x-v)*(fx-fw);    (Repository): Elapsed time after each iteration is now output. It
       p=(x-v)*q-(x-w)*r;    helps to forecast when convergence will be reached. Elapsed time
       q=2.0*(q-r);    is stamped in powell.  We created a new html file for the graphs
       if (q > 0.0) p = -p;    concerning matrix of covariance. It has extension -cov.htm.
       q=fabs(q);  
       etemp=e;    Revision 1.90  2003/06/24 12:34:15  brouard
       e=d;    (Module): Some bugs corrected for windows. Also, when
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    mle=-1 a template is output in file "or"mypar.txt with the design
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    of the covariance matrix to be input.
       else {  
         d=p/q;    Revision 1.89  2003/06/24 12:30:52  brouard
         u=x+d;    (Module): Some bugs corrected for windows. Also, when
         if (u-a < tol2 || b-u < tol2)    mle=-1 a template is output in file "or"mypar.txt with the design
           d=SIGN(tol1,xm-x);    of the covariance matrix to be input.
       }  
     } else {    Revision 1.88  2003/06/23 17:54:56  brouard
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    Revision 1.87  2003/06/18 12:26:01  brouard
     fu=(*f)(u);    Version 0.96
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;    Revision 1.86  2003/06/17 20:04:08  brouard
       SHFT(v,w,x,u)    (Module): Change position of html and gnuplot routines and added
         SHFT(fv,fw,fx,fu)    routine fileappend.
         } else {  
           if (u < x) a=u; else b=u;    Revision 1.85  2003/06/17 13:12:43  brouard
           if (fu <= fw || w == x) {    * imach.c (Repository): Check when date of death was earlier that
             v=w;    current date of interview. It may happen when the death was just
             w=u;    prior to the death. In this case, dh was negative and likelihood
             fv=fw;    was wrong (infinity). We still send an "Error" but patch by
             fw=fu;    assuming that the date of death was just one stepm after the
           } else if (fu <= fv || v == x || v == w) {    interview.
             v=u;    (Repository): Because some people have very long ID (first column)
             fv=fu;    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)
   }    (Repository): No more line truncation errors.
   nrerror("Too many iterations in brent");  
   *xmin=x;    Revision 1.84  2003/06/13 21:44:43  brouard
   return fx;    * imach.c (Repository): Replace "freqsummary" at a correct
 }    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 /****************** mnbrak ***********************/    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   double ulim,u,r,q, dum;  
   double fu;    Revision 1.82  2003/06/05 15:57:20  brouard
      Add log in  imach.c and  fullversion number is now printed.
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  */
   if (*fb > *fa) {  /*
     SHFT(dum,*ax,*bx,dum)     Interpolated Markov Chain
       SHFT(dum,*fb,*fa,dum)  
       }    Short summary of the programme:
   *cx=(*bx)+GOLD*(*bx-*ax);    
   *fc=(*func)(*cx);    This program computes Healthy Life Expectancies from
   while (*fb > *fc) {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     r=(*bx-*ax)*(*fb-*fc);    first survey ("cross") where individuals from different ages are
     q=(*bx-*cx)*(*fb-*fa);    interviewed on their health status or degree of disability (in the
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    case of a health survey which is our main interest) -2- at least a
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    second wave of interviews ("longitudinal") which measure each change
     ulim=(*bx)+GLIMIT*(*cx-*bx);    (if any) in individual health status.  Health expectancies are
     if ((*bx-u)*(u-*cx) > 0.0) {    computed from the time spent in each health state according to a
       fu=(*func)(u);    model. More health states you consider, more time is necessary to reach the
     } else if ((*cx-u)*(u-ulim) > 0.0) {    Maximum Likelihood of the parameters involved in the model.  The
       fu=(*func)(u);    simplest model is the multinomial logistic model where pij is the
       if (fu < *fc) {    probability to be observed in state j at the second wave
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    conditional to be observed in state i at the first wave. Therefore
           SHFT(*fb,*fc,fu,(*func)(u))    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
           }    'age' is age and 'sex' is a covariate. If you want to have a more
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    complex model than "constant and age", you should modify the program
       u=ulim;    where the markup *Covariates have to be included here again* invites
       fu=(*func)(u);    you to do it.  More covariates you add, slower the
     } else {    convergence.
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);    The advantage of this computer programme, compared to a simple
     }    multinomial logistic model, is clear when the delay between waves is not
     SHFT(*ax,*bx,*cx,u)    identical for each individual. Also, if a individual missed an
       SHFT(*fa,*fb,*fc,fu)    intermediate interview, the information is lost, but taken into
       }    account using an interpolation or extrapolation.  
 }  
     hPijx is the probability to be observed in state i at age x+h
 /*************** linmin ************************/    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
 int ncom;    states. This elementary transition (by month, quarter,
 double *pcom,*xicom;    semester or year) is modelled as a multinomial logistic.  The hPx
 double (*nrfunc)(double []);    matrix is simply the matrix product of nh*stepm elementary matrices
      and the contribution of each individual to the likelihood is simply
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    hPijx.
 {  
   double brent(double ax, double bx, double cx,    Also this programme outputs the covariance matrix of the parameters but also
                double (*f)(double), double tol, double *xmin);    of the life expectancies. It also computes the period (stable) prevalence. 
   double f1dim(double x);    
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
               double *fc, double (*func)(double));             Institut national d'études démographiques, Paris.
   int j;    This software have been partly granted by Euro-REVES, a concerted action
   double xx,xmin,bx,ax;    from the European Union.
   double fx,fb,fa;    It is copyrighted identically to a GNU software product, ie programme and
      software can be distributed freely for non commercial use. Latest version
   ncom=n;    can be accessed at http://euroreves.ined.fr/imach .
   pcom=vector(1,n);  
   xicom=vector(1,n);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   nrfunc=func;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   for (j=1;j<=n;j++) {    
     pcom[j]=p[j];    **********************************************************************/
     xicom[j]=xi[j];  /*
   }    main
   ax=0.0;    read parameterfile
   xx=1.0;    read datafile
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    concatwav
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    freqsummary
 #ifdef DEBUG    if (mle >= 1)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      mlikeli
 #endif    print results files
   for (j=1;j<=n;j++) {    if mle==1 
     xi[j] *= xmin;       computes hessian
     p[j] += xi[j];    read end of parameter file: agemin, agemax, bage, fage, estepm
   }        begin-prev-date,...
   free_vector(xicom,1,n);    open gnuplot file
   free_vector(pcom,1,n);    open html file
 }    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
      for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 /*************** powell ************************/                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      freexexit2 possible for memory heap.
             double (*func)(double []))  
 {    h Pij x                         | pij_nom  ficrestpij
   void linmin(double p[], double xi[], int n, double *fret,     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
               double (*func)(double []));         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   int i,ibig,j;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   double *xits;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   pt=vector(1,n);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   ptt=vector(1,n);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   xit=vector(1,n);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   xits=vector(1,n);  
   *fret=(*func)(p);    forecasting if prevfcast==1 prevforecast call prevalence()
   for (j=1;j<=n;j++) pt[j]=p[j];    health expectancies
   for (*iter=1;;++(*iter)) {    Variance-covariance of DFLE
     fp=(*fret);    prevalence()
     ibig=0;     movingaverage()
     del=0.0;    varevsij() 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    if popbased==1 varevsij(,popbased)
     for (i=1;i<=n;i++)    total life expectancies
       printf(" %d %.12f",i, p[i]);    Variance of period (stable) prevalence
     printf("\n");   end
     for (i=1;i<=n;i++) {  */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  #define POWELL /* Instead of NLOPT */
 #ifdef DEBUG  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
       printf("fret=%lf \n",*fret);  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
 #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 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
     }  char fullversion[]="$Revision$ $Date$"; 
   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=0, l2=0;                             /* 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++) {  #ifdef WIN32
         po[i][j][h]=newm[i][j];      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  #else
          */          if (getcwd(dirc, FILENAME_MAX) == NULL) {
       }  #endif
   } /* end h */        return( GLOCK_ERROR_GETCWD );
   return po;      }
 }      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
 /*************** log-likelihood *************/      ss++;                               /* after this, the filename */
 double func( double *x)      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i, ii, j, k, mi, d, kk;      strcpy( name, ss );         /* save file name */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   double **out;      dirc[l1-l2] = '\0';                 /* add zero */
   double sw; /* Sum of weights */      printf(" DIRC2 = %s \n",dirc);
   double lli; /* Individual log likelihood */    }
   long ipmx;    /* We add a separator at the end of dirc if not exists */
   /*extern weight */    l1 = strlen( dirc );                  /* length of directory */
   /* We are differentiating ll according to initial status */    if( dirc[l1-1] != DIRSEPARATOR ){
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      dirc[l1] =  DIRSEPARATOR;
   /*for(i=1;i<imx;i++)      dirc[l1+1] = 0; 
     printf(" %d\n",s[4][i]);      printf(" DIRC3 = %s \n",dirc);
   */    }
   cov[1]=1.;    ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
   for(k=1; k<=nlstate; k++) ll[k]=0.;      ss++;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      strcpy(ext,ss);                     /* save extension */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      l1= strlen( name);
     for(mi=1; mi<= wav[i]-1; mi++){      l2= strlen(ss)+1;
       for (ii=1;ii<=nlstate+ndeath;ii++)      strncpy( finame, name, l1-l2);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      finame[l1-l2]= 0;
       for(d=0; d<dh[mi][i]; d++){    }
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return( 0 );                          /* we're done */
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  
          /******************************************/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  void replace_back_to_slash(char *s, char*t)
         savm=oldm;  {
         oldm=newm;    int i;
            int lg=0;
            i=0;
       } /* end mult */    lg=strlen(t);
          for(i=0; i<= lg; i++) {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      (s[i] = t[i]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      if (t[i]== '\\') s[i]='/';
       ipmx +=1;    }
       sw += weight[i];  }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  char *trimbb(char *out, char *in)
   } /* end of individual */  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     char *s;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    s=out;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    while (*in != '\0'){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   return -l;        in++;
 }      }
       *out++ = *in++;
     }
 /*********** Maximum Likelihood Estimation ***************/    *out='\0';
     return s;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  }
 {  
   int i,j, iter;  char *cutl(char *blocc, char *alocc, char *in, char occ)
   double **xi,*delti;  {
   double fret;    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
   xi=matrix(1,npar,1,npar);       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   for (i=1;i<=npar;i++)       gives blocc="abcdef2ghi" and alocc="j".
     for (j=1;j<=npar;j++)       If occ is not found blocc is null and alocc is equal to in. Returns blocc
       xi[i][j]=(i==j ? 1.0 : 0.0);    */
   printf("Powell\n");    char *s, *t;
   powell(p,xi,npar,ftol,&iter,&fret,func);    t=in;s=in;
     while ((*in != occ) && (*in != '\0')){
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      *alocc++ = *in++;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    }
     if( *in == occ){
 }      *(alocc)='\0';
       s=++in;
 /**** Computes Hessian and covariance matrix ***/    }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))   
 {    if (s == t) {/* occ not found */
   double  **a,**y,*x,pd;      *(alocc-(in-s))='\0';
   double **hess;      in=s;
   int i, j,jk;    }
   int *indx;    while ( *in != '\0'){
       *blocc++ = *in++;
   double hessii(double p[], double delta, int theta, double delti[]);    }
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;    *blocc='\0';
   void ludcmp(double **a, int npar, int *indx, double *d) ;    return t;
   }
   hess=matrix(1,npar,1,npar);  char *cutv(char *blocc, char *alocc, char *in, char occ)
   {
   printf("\nCalculation of the hessian matrix. Wait...\n");    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   for (i=1;i<=npar;i++){       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     printf("%d",i);fflush(stdout);       gives blocc="abcdef2ghi" and alocc="j".
     hess[i][i]=hessii(p,ftolhess,i,delti);       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     /*printf(" %f ",p[i]);*/    */
     /*printf(" %lf ",hess[i][i]);*/    char *s, *t;
   }    t=in;s=in;
      while (*in != '\0'){
   for (i=1;i<=npar;i++) {      while( *in == occ){
     for (j=1;j<=npar;j++)  {        *blocc++ = *in++;
       if (j>i) {        s=in;
         printf(".%d%d",i,j);fflush(stdout);      }
         hess[i][j]=hessij(p,delti,i,j);      *blocc++ = *in++;
         hess[j][i]=hess[i][j];        }
         /*printf(" %lf ",hess[i][j]);*/    if (s == t) /* occ not found */
       }      *(blocc-(in-s))='\0';
     }    else
   }      *(blocc-(in-s)-1)='\0';
   printf("\n");    in=s;
     while ( *in != '\0'){
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      *alocc++ = *in++;
      }
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);    *alocc='\0';
   x=vector(1,npar);    return s;
   indx=ivector(1,npar);  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  int nbocc(char *s, char occ)
   ludcmp(a,npar,indx,&pd);  {
     int i,j=0;
   for (j=1;j<=npar;j++) {    int lg=20;
     for (i=1;i<=npar;i++) x[i]=0;    i=0;
     x[j]=1;    lg=strlen(s);
     lubksb(a,npar,indx,x);    for(i=0; i<= lg; i++) {
     for (i=1;i<=npar;i++){    if  (s[i] == occ ) j++;
       matcov[i][j]=x[i];    }
     }    return j;
   }  }
   
   printf("\n#Hessian matrix#\n");  /* void cutv(char *u,char *v, char*t, char occ) */
   for (i=1;i<=npar;i++) {  /* { */
     for (j=1;j<=npar;j++) {  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       printf("%.3e ",hess[i][j]);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     }  /*      gives u="abcdef2ghi" and v="j" *\/ */
     printf("\n");  /*   int i,lg,j,p=0; */
   }  /*   i=0; */
   /*   lg=strlen(t); */
   /* Recompute Inverse */  /*   for(j=0; j<=lg-1; j++) { */
   for (i=1;i<=npar;i++)  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /*   } */
   ludcmp(a,npar,indx,&pd);  
   /*   for(j=0; j<p; j++) { */
   /*  printf("\n#Hessian matrix recomputed#\n");  /*     (u[j] = t[j]); */
   /*   } */
   for (j=1;j<=npar;j++) {  /*      u[p]='\0'; */
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  /*    for(j=0; j<= lg; j++) { */
     lubksb(a,npar,indx,x);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     for (i=1;i<=npar;i++){  /*   } */
       y[i][j]=x[i];  /* } */
       printf("%.3e ",y[i][j]);  
     }  #ifdef _WIN32
     printf("\n");  char * strsep(char **pp, const char *delim)
   }  {
   */    char *p, *q;
            
   free_matrix(a,1,npar,1,npar);    if ((p = *pp) == NULL)
   free_matrix(y,1,npar,1,npar);      return 0;
   free_vector(x,1,npar);    if ((q = strpbrk (p, delim)) != NULL)
   free_ivector(indx,1,npar);    {
   free_matrix(hess,1,npar,1,npar);      *pp = q + 1;
       *q = '\0';
     }
 }    else
       *pp = 0;
 /*************** hessian matrix ****************/    return p;
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  #endif
   int i;  
   int l=1, lmax=20;  /********************** nrerror ********************/
   double k1,k2;  
   double p2[NPARMAX+1];  void nrerror(char error_text[])
   double res;  {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    fprintf(stderr,"ERREUR ...\n");
   double fx;    fprintf(stderr,"%s\n",error_text);
   int k=0,kmax=10;    exit(EXIT_FAILURE);
   double l1;  }
   /*********************** vector *******************/
   fx=func(x);  double *vector(int nl, int nh)
   for (i=1;i<=npar;i++) p2[i]=x[i];  {
   for(l=0 ; l <=lmax; l++){    double *v;
     l1=pow(10,l);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     delts=delt;    if (!v) nrerror("allocation failure in vector");
     for(k=1 ; k <kmax; k=k+1){    return v-nl+NR_END;
       delt = delta*(l1*k);  }
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  /************************ free vector ******************/
       p2[theta]=x[theta]-delt;  void free_vector(double*v, int nl, int nh)
       k2=func(p2)-fx;  {
       /*res= (k1-2.0*fx+k2)/delt/delt; */    free((FREE_ARG)(v+nl-NR_END));
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  }
        
 #ifdef DEBUG  /************************ivector *******************************/
       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);  int *ivector(long nl,long nh)
 #endif  {
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    int *v;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         k=kmax;    if (!v) nrerror("allocation failure in ivector");
       }    return v-nl+NR_END;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  }
         k=kmax; l=lmax*10.;  
       }  /******************free ivector **************************/
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  void free_ivector(int *v, long nl, long nh)
         delts=delt;  {
       }    free((FREE_ARG)(v+nl-NR_END));
     }  }
   }  
   delti[theta]=delts;  /************************lvector *******************************/
   return res;  long *lvector(long nl,long nh)
    {
 }    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 double hessij( double x[], double delti[], int thetai,int thetaj)    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   int i;  }
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;  /******************free lvector **************************/
   double p2[NPARMAX+1];  void free_lvector(long *v, long nl, long nh)
   int k;  {
     free((FREE_ARG)(v+nl-NR_END));
   fx=func(x);  }
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  /******************* imatrix *******************************/
     p2[thetai]=x[thetai]+delti[thetai]/k;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     k1=func(p2)-fx;  { 
      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;    
     k2=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; 
     k3=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 */ 
     k4=func(p2)-fx;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 #ifdef DEBUG    m[nrl] += NR_END; 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    m[nrl] -= ncl; 
 #endif    
   }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   return res;    
 }    /* return pointer to array of pointers to rows */ 
     return m; 
 /************** Inverse of matrix **************/  } 
 void ludcmp(double **a, int n, int *indx, double *d)  
 {  /****************** free_imatrix *************************/
   int i,imax,j,k;  void free_imatrix(m,nrl,nrh,ncl,nch)
   double big,dum,sum,temp;        int **m;
   double *vv;        long nch,ncl,nrh,nrl; 
         /* free an int matrix allocated by imatrix() */ 
   vv=vector(1,n);  { 
   *d=1.0;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   for (i=1;i<=n;i++) {    free((FREE_ARG) (m+nrl-NR_END)); 
     big=0.0;  } 
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;  /******************* matrix *******************************/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  double **matrix(long nrl, long nrh, long ncl, long nch)
     vv[i]=1.0/big;  {
   }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   for (j=1;j<=n;j++) {    double **m;
     for (i=1;i<j;i++) {  
       sum=a[i][j];    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    if (!m) nrerror("allocation failure 1 in matrix()");
       a[i][j]=sum;    m += NR_END;
     }    m -= nrl;
     big=0.0;  
     for (i=j;i<=n;i++) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       sum=a[i][j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for (k=1;k<j;k++)    m[nrl] += NR_END;
         sum -= a[i][k]*a[k][j];    m[nrl] -= ncl;
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         big=dum;    return m;
         imax=i;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
       }  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     }  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     if (j != imax) {     */
       for (k=1;k<=n;k++) {  }
         dum=a[imax][k];  
         a[imax][k]=a[j][k];  /*************************free matrix ************************/
         a[j][k]=dum;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       }  {
       *d = -(*d);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       vv[imax]=vv[j];    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  /******************* ma3x *******************************/
     if (j != n) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       dum=1.0/(a[j][j]);  {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     }    double ***m;
   }  
   free_vector(vv,1,n);  /* Doesn't work */    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 ;    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 void lubksb(double **a, int n, int *indx, double b[])  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   int i,ii=0,ip,j;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double sum;    m[nrl] += NR_END;
      m[nrl] -= ncl;
   for (i=1;i<=n;i++) {  
     ip=indx[i];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     sum=b[ip];  
     b[ip]=b[i];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (ii)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    m[nrl][ncl] += NR_END;
     else if (sum) ii=i;    m[nrl][ncl] -= nll;
     b[i]=sum;    for (j=ncl+1; j<=nch; j++) 
   }      m[nrl][j]=m[nrl][j-1]+nlay;
   for (i=n;i>=1;i--) {    
     sum=b[i];    for (i=nrl+1; i<=nrh; i++) {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     b[i]=sum/a[i][i];      for (j=ncl+1; j<=nch; j++) 
   }        m[i][j]=m[i][j-1]+nlay;
 }    }
     return m; 
 /************ Frequencies ********************/    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 {  /* Some frequencies */    */
    }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  /*************************free ma3x ************************/
   double *pp;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double pos, k2, dateintsum=0,k2cpt=0;  {
   FILE *ficresp;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   char fileresp[FILENAMELENGTH];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
   pp=vector(1,nlstate);  }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");  /*************** function subdirf ***********/
   strcat(fileresp,fileres);  char *subdirf(char fileres[])
   if((ficresp=fopen(fileresp,"w"))==NULL) {  {
     printf("Problem with prevalence resultfile: %s\n", fileresp);    /* Caution optionfilefiname is hidden */
     exit(0);    strcpy(tmpout,optionfilefiname);
   }    strcat(tmpout,"/"); /* Add to the right */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    strcat(tmpout,fileres);
   j1=0;    return tmpout;
   }
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
   for(k1=1; k1<=j;k1++){  {
    for(i1=1; i1<=ncodemax[k1];i1++){    
        j1++;    /* Caution optionfilefiname is hidden */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    strcpy(tmpout,optionfilefiname);
          scanf("%d", i);*/    strcat(tmpout,"/");
         for (i=-1; i<=nlstate+ndeath; i++)      strcat(tmpout,preop);
          for (jk=-1; jk<=nlstate+ndeath; jk++)      strcat(tmpout,fileres);
            for(m=agemin; m <= agemax+3; m++)    return tmpout;
              freq[i][jk][m]=0;  }
   
         dateintsum=0;  /*************** function subdirf3 ***********/
         k2cpt=0;  char *subdirf3(char fileres[], char *preop, char *preop2)
        for (i=1; i<=imx; i++) {  {
          bool=1;    
          if  (cptcovn>0) {    /* Caution optionfilefiname is hidden */
            for (z1=1; z1<=cptcoveff; z1++)    strcpy(tmpout,optionfilefiname);
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    strcat(tmpout,"/");
                bool=0;    strcat(tmpout,preop);
          }    strcat(tmpout,preop2);
          if (bool==1) {    strcat(tmpout,fileres);
            for(m=firstpass; m<=lastpass; m++){    return tmpout;
              k2=anint[m][i]+(mint[m][i]/12.);  }
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  
                if(agev[m][i]==0) agev[m][i]=agemax+1;  char *asc_diff_time(long time_sec, char ascdiff[])
                if(agev[m][i]==1) agev[m][i]=agemax+2;  {
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    long sec_left, days, hours, minutes;
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    days = (time_sec) / (60*60*24);
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    sec_left = (time_sec) % (60*60*24);
                  dateintsum=dateintsum+k2;    hours = (sec_left) / (60*60) ;
                  k2cpt++;    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);  
            }    return ascdiff;
          }  }
        }  
          /***************** f1dim *************************/
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  extern int ncom; 
   extern double *pcom,*xicom;
         if  (cptcovn>0) {  extern double (*nrfunc)(double []); 
          fprintf(ficresp, "\n#********** Variable ");   
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  double f1dim(double x) 
        fprintf(ficresp, "**********\n#");  { 
         }    int j; 
        for(i=1; i<=nlstate;i++)    double f;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double *xt; 
        fprintf(ficresp, "\n");   
            xt=vector(1,ncom); 
   for(i=(int)agemin; i <= (int)agemax+3; i++){    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     if(i==(int)agemax+3)    f=(*nrfunc)(xt); 
       printf("Total");    free_vector(xt,1,ncom); 
     else    return f; 
       printf("Age %d", i);  } 
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  /*****************brent *************************/
         pp[jk] += freq[jk][m][i];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     for(jk=1; jk <=nlstate ; jk++){    int iter; 
       for(m=-1, pos=0; m <=0 ; m++)    double a,b,d,etemp;
         pos += freq[jk][m][i];    double fu=0,fv,fw,fx;
       if(pp[jk]>=1.e-10)    double ftemp=0.;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       else    double e=0.0; 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);   
     }    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
      for(jk=1; jk <=nlstate ; jk++){    x=w=v=bx; 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    fw=fv=fx=(*f)(x); 
         pp[jk] += freq[jk][m][i];    for (iter=1;iter<=ITMAX;iter++) { 
      }      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     for(jk=1,pos=0; jk <=nlstate ; jk++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       pos += pp[jk];      printf(".");fflush(stdout);
     for(jk=1; jk <=nlstate ; jk++){      fprintf(ficlog,".");fflush(ficlog);
       if(pos>=1.e-5)  #ifdef DEBUGBRENT
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*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);
       else      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);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       if( i <= (int) agemax){  #endif
         if(pos>=1.e-5){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        *xmin=x; 
           probs[i][jk][j1]= pp[jk]/pos;        return fx; 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      } 
         }      ftemp=fu;
       else      if (fabs(e) > tol1) { 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        r=(x-w)*(fx-fv); 
       }        q=(x-v)*(fx-fw); 
     }        p=(x-v)*q-(x-w)*r; 
     for(jk=-1; jk <=nlstate+ndeath; jk++)        q=2.0*(q-r); 
       for(m=-1; m <=nlstate+ndeath; m++)        if (q > 0.0) p = -p; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        q=fabs(q); 
     if(i <= (int) agemax)        etemp=e; 
       fprintf(ficresp,"\n");        e=d; 
     printf("\n");        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }        else { 
  }          d=p/q; 
   dateintmean=dateintsum/k2cpt;          u=x+d; 
            if (u-a < tol2 || b-u < tol2) 
   fclose(ficresp);            d=SIGN(tol1,xm-x); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        } 
   free_vector(pp,1,nlstate);      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   /* End of Freq */      } 
 }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
 /************ Prevalence ********************/      if (fu <= fx) { 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        if (u >= x) a=x; else b=x; 
 {  /* Some frequencies */        SHFT(v,w,x,u) 
          SHFT(fv,fw,fx,fu) 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      } else { 
   double ***freq; /* Frequencies */        if (u < x) a=u; else b=u; 
   double *pp;        if (fu <= fw || w == x) { 
   double pos, k2;          v=w; 
           w=u; 
   pp=vector(1,nlstate);          fv=fw; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          fw=fu; 
          } else if (fu <= fv || v == x || v == w) { 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          v=u; 
   j1=0;          fv=fu; 
          } 
   j=cptcoveff;      } 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    } 
      nrerror("Too many iterations in brent"); 
  for(k1=1; k1<=j;k1++){    *xmin=x; 
     for(i1=1; i1<=ncodemax[k1];i1++){    return fx; 
       j1++;  } 
    
       for (i=-1; i<=nlstate+ndeath; i++)    /****************** mnbrak ***********************/
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
             freq[i][jk][m]=0;              double (*func)(double)) 
        { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
       for (i=1; i<=imx; i++) {  the downhill direction (defined by the function as evaluated at the initial points) and returns
         bool=1;  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
         if  (cptcovn>0) {  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
           for (z1=1; z1<=cptcoveff; z1++)     */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double ulim,u,r,q, dum;
               bool=0;    double fu; 
         }   
         if (bool==1) {    *fa=(*func)(*ax); 
           for(m=firstpass; m<=lastpass; m++){    *fb=(*func)(*bx); 
             k2=anint[m][i]+(mint[m][i]/12.);    if (*fb > *fa) { 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      SHFT(dum,*ax,*bx,dum) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      SHFT(dum,*fb,*fa,dum) 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    } 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    *cx=(*bx)+GOLD*(*bx-*ax); 
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    *fc=(*func)(*cx); 
             }  #ifdef DEBUG
           }    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
         }    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
       }  #endif
         for(i=(int)agemin; i <= (int)agemax+3; i++){    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
           for(jk=1; jk <=nlstate ; jk++){      r=(*bx-*ax)*(*fb-*fc); 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      q=(*bx-*cx)*(*fb-*fa); 
               pp[jk] += freq[jk][m][i];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
           }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
           for(jk=1; jk <=nlstate ; jk++){      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
             for(m=-1, pos=0; m <=0 ; m++)      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
             pos += freq[jk][m][i];        fu=(*func)(u); 
         }  #ifdef DEBUG
                /* f(x)=A(x-u)**2+f(u) */
          for(jk=1; jk <=nlstate ; jk++){        double A, fparabu; 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
              pp[jk] += freq[jk][m][i];        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);
                  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);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        /* And thus,it can be that fu > *fc even if fparabu < *fc */
         /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
          for(jk=1; jk <=nlstate ; jk++){                    (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
            if( i <= (int) agemax){        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
              if(pos>=1.e-5){  #endif 
                probs[i][jk][j1]= pp[jk]/pos;  #ifdef MNBRAKORIGINAL
              }  #else
            }        if (fu > *fc) {
          }  #ifdef DEBUG
                  printf("mnbrak4  fu > fc \n");
         }        fprintf(ficlog, "mnbrak4 fu > fc\n");
     }  #endif
   }          /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/  */
            /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
            dum=u; /* Shifting c and u */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          u = *cx;
   free_vector(pp,1,nlstate);          *cx = dum;
            dum = fu;
 }  /* End of Freq */          fu = *fc;
           *fc =dum;
 /************* Waves Concatenation ***************/        } else { /* end */
   #ifdef DEBUG
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        printf("mnbrak3  fu < fc \n");
 {        fprintf(ficlog, "mnbrak3 fu < fc\n");
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  #endif
      Death is a valid wave (if date is known).          dum=u; /* Shifting c and u */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          u = *cx;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          *cx = dum;
      and mw[mi+1][i]. dh depends on stepm.          dum = fu;
      */          fu = *fc;
           *fc =dum;
   int i, mi, m;        }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  #endif
      double sum=0., jmean=0.;*/      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   #ifdef DEBUG
   int j, k=0,jk, ju, jl;        printf("mnbrak2  u after c but before ulim\n");
   double sum=0.;        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
   jmin=1e+5;  #endif
   jmax=-1;        fu=(*func)(u); 
   jmean=0.;        if (fu < *fc) { 
   for(i=1; i<=imx; i++){  #ifdef DEBUG
     mi=0;        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
     m=firstpass;        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
     while(s[m][i] <= nlstate){  #endif
       if(s[m][i]>=1)          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         mw[++mi][i]=m;          SHFT(*fb,*fc,fu,(*func)(u)) 
       if(m >=lastpass)        } 
         break;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
       else  #ifdef DEBUG
         m++;        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
     }/* end while */        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
     if (s[m][i] > nlstate){  #endif
       mi++;     /* Death is another wave */        u=ulim; 
       /* if(mi==0)  never been interviewed correctly before death */        fu=(*func)(u); 
          /* Only death is a correct wave */      } else { /* u could be left to b (if r > q parabola has a maximum) */
       mw[mi][i]=m;  #ifdef DEBUG
     }        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
         fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
     wav[i]=mi;  #endif
     if(mi==0)        u=(*cx)+GOLD*(*cx-*bx); 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        fu=(*func)(u); 
   }      } /* end tests */
       SHFT(*ax,*bx,*cx,u) 
   for(i=1; i<=imx; i++){      SHFT(*fa,*fb,*fc,fu) 
     for(mi=1; mi<wav[i];mi++){  #ifdef DEBUG
       if (stepm <=0)        printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
         dh[mi][i]=1;        fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
       else{  #endif
         if (s[mw[mi+1][i]][i] > nlstate) {    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
           if (agedc[i] < 2*AGESUP) {  } 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */  /*************** linmin ************************/
           k=k+1;  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
           if (j >= jmax) jmax=j;  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
           if (j <= jmin) jmin=j;  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
           sum=sum+j;  the value of func at the returned location p . This is actually all accomplished by calling the
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  routines mnbrak and brent .*/
           }  int ncom; 
         }  double *pcom,*xicom;
         else{  double (*nrfunc)(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,double (*func)(double [])) 
           if (j >= jmax) jmax=j;  { 
           else if (j <= jmin)jmin=j;    double brent(double ax, double bx, double cx, 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */                 double (*f)(double), double tol, double *xmin); 
           sum=sum+j;    double f1dim(double x); 
         }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         jk= j/stepm;                double *fc, double (*func)(double)); 
         jl= j -jk*stepm;    int j; 
         ju= j -(jk+1)*stepm;    double xx,xmin,bx,ax; 
         if(jl <= -ju)    double fx,fb,fa;
           dh[mi][i]=jk;   
         else    ncom=n; 
           dh[mi][i]=jk+1;    pcom=vector(1,n); 
         if(dh[mi][i]==0)    xicom=vector(1,n); 
           dh[mi][i]=1; /* At least one step */    nrfunc=func; 
       }    for (j=1;j<=n;j++) { 
     }      pcom[j]=p[j]; 
   }      xicom[j]=xi[j]; 
   jmean=sum/k;    } 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    ax=0.0; 
  }    xx=1.0; 
 /*********** Tricode ****************************/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
 void tricode(int *Tvar, int **nbcode, int imx)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
 {  #ifdef DEBUG
   int Ndum[20],ij=1, k, j, i;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   int cptcode=0;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   cptcoveff=0;  #endif
      for (j=1;j<=n;j++) { 
   for (k=0; k<19; k++) Ndum[k]=0;      xi[j] *= xmin; 
   for (k=1; k<=7; k++) ncodemax[k]=0;      p[j] += xi[j]; 
     } 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    free_vector(xicom,1,n); 
     for (i=1; i<=imx; i++) {    free_vector(pcom,1,n); 
       ij=(int)(covar[Tvar[j]][i]);  } 
       Ndum[ij]++;  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;  /*************** powell ************************/
     }  /*
   Minimization of a function func of n variables. Input consists of an initial starting point
     for (i=0; i<=cptcode; i++) {  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
       if(Ndum[i]!=0) ncodemax[j]++;  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
     }  such that failure to decrease by more than this amount on one iteration signals doneness. On
     ij=1;  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
   function value at p , and iter is the number of iterations taken. The routine linmin is used.
    */
     for (i=1; i<=ncodemax[j]; i++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for (k=0; k<=19; k++) {              double (*func)(double [])) 
         if (Ndum[k] != 0) {  { 
           nbcode[Tvar[j]][ij]=k;    void linmin(double p[], double xi[], int n, double *fret, 
           ij++;                double (*func)(double [])); 
         }    int i,ibig,j; 
         if (ij > ncodemax[j]) break;    double del,t,*pt,*ptt,*xit;
       }      double directest;
     }    double fp,fptt;
   }      double *xits;
     int niterf, itmp;
  for (k=0; k<19; k++) Ndum[k]=0;  
     pt=vector(1,n); 
  for (i=1; i<=ncovmodel-2; i++) {    ptt=vector(1,n); 
       ij=Tvar[i];    xit=vector(1,n); 
       Ndum[ij]++;    xits=vector(1,n); 
     }    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
  ij=1;      rcurr_time = time(NULL);  
  for (i=1; i<=10; i++) {    for (*iter=1;;++(*iter)) { 
    if((Ndum[i]!=0) && (i<=ncov)){      fp=(*fret); 
      Tvaraff[ij]=i;      ibig=0; 
      ij++;      del=0.0; 
    }      rlast_time=rcurr_time;
  }      /* (void) gettimeofday(&curr_time,&tzp); */
        rcurr_time = time(NULL);  
     cptcoveff=ij-1;      curr_time = *localtime(&rcurr_time);
 }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
 /*********** Health Expectancies ****************/  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
      for (i=1;i<=n;i++) {
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        printf(" %d %.12f",i, p[i]);
 {        fprintf(ficlog," %d %.12lf",i, p[i]);
   /* Health expectancies */        fprintf(ficrespow," %.12lf", p[i]);
   int i, j, nhstepm, hstepm, h, nstepm, k;      }
   double age, agelim,hf;      printf("\n");
   double ***p3mat;      fprintf(ficlog,"\n");
        fprintf(ficrespow,"\n");fflush(ficrespow);
   fprintf(ficreseij,"# Health expectancies\n");      if(*iter <=3){
   fprintf(ficreseij,"# Age");        tml = *localtime(&rcurr_time);
   for(i=1; i<=nlstate;i++)        strcpy(strcurr,asctime(&tml));
     for(j=1; j<=nlstate;j++)        rforecast_time=rcurr_time; 
       fprintf(ficreseij," %1d-%1d",i,j);        itmp = strlen(strcurr);
   fprintf(ficreseij,"\n");        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
   k=1;             /* For example stepm=6 months */        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */        for(niterf=10;niterf<=30;niterf+=10){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
      nhstepm is the number of hstepm from age to agelim          forecast_time = *localtime(&rforecast_time);
      nstepm is the number of stepm from age to agelin.          strcpy(strfor,asctime(&forecast_time));
      Look at hpijx to understand the reason of that which relies in memory size          itmp = strlen(strfor);
      and note for a fixed period like k years */          if(strfor[itmp-1]=='\n')
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          strfor[itmp-1]='\0';
      survival function given by stepm (the optimization length). Unfortunately it          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);
      means that if the survival funtion is printed only each two years of age and if          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);
      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.      }
   */      for (i=1;i<=n;i++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   agelim=AGESUP;  #ifdef DEBUG
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     /* nhstepm age range expressed in number of stepm */            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  #endif
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        printf("%d",i);fflush(stdout);
     if (stepm >= YEARM) hstepm=1;        fprintf(ficlog,"%d",i);fflush(ficlog);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored                                         because that direction will be replaced unless the gain del is small
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                                        in comparison with the 'probable' gain, mu^2, with the last average direction.
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                                          Unless the n directions are conjugate some gain in the determinant may be obtained
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                                        with the new direction.
     for(i=1; i<=nlstate;i++)                                        */
       for(j=1; j<=nlstate;j++)          del=fabs(fptt-(*fret)); 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          ibig=i; 
           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]);*/  #ifdef DEBUG
         }        printf("%d %.12e",i,(*fret));
     fprintf(ficreseij,"%3.0f",age );        fprintf(ficlog,"%d %.12e",i,(*fret));
     for(i=1; i<=nlstate;i++)        for (j=1;j<=n;j++) {
       for(j=1; j<=nlstate;j++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);          printf(" x(%d)=%.12e",j,xit[j]);
       }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     fprintf(ficreseij,"\n");        }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=1;j<=n;j++) {
   }          printf(" p(%d)=%.12e",j,p[j]);
 }          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
         }
 /************ Variance ******************/        printf("\n");
 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)        fprintf(ficlog,"\n");
 {  #endif
   /* Variance of health expectancies */      } /* end i */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
   double **newm;  #ifdef DEBUG
   double **dnewm,**doldm;        int k[2],l;
   int i, j, nhstepm, hstepm, h;        k[0]=1;
   int k, cptcode;        k[1]=-1;
   double *xp;        printf("Max: %.12e",(*func)(p));
   double **gp, **gm;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double ***gradg, ***trgradg;        for (j=1;j<=n;j++) {
   double ***p3mat;          printf(" %.12e",p[j]);
   double age,agelim;          fprintf(ficlog," %.12e",p[j]);
   int theta;        }
         printf("\n");
    fprintf(ficresvij,"# Covariances of life expectancies\n");        fprintf(ficlog,"\n");
   fprintf(ficresvij,"# Age");        for(l=0;l<=1;l++) {
   for(i=1; i<=nlstate;i++)          for (j=1;j<=n;j++) {
     for(j=1; j<=nlstate;j++)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   fprintf(ficresvij,"\n");            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
   xp=vector(1,npar);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   dnewm=matrix(1,nlstate,1,npar);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   doldm=matrix(1,nlstate,1,nlstate);        }
    #endif
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;        free_vector(xit,1,n); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        free_vector(xits,1,n); 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        free_vector(ptt,1,n); 
     if (stepm >= YEARM) hstepm=1;        free_vector(pt,1,n); 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        return; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     gp=matrix(0,nhstepm,1,nlstate);      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
     gm=matrix(0,nhstepm,1,nlstate);        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
     for(theta=1; theta <=npar; theta++){        pt[j]=p[j]; 
       for(i=1; i<=npar; i++){ /* Computes gradient */      } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      fptt=(*func)(ptt); /* f_3 */
       }      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       if (popbased==1) {        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         for(i=1; i<=nlstate;i++)        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
           prlim[i][i]=probs[(int)age][i][ij];        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
       }        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
    #ifdef NRCORIGINAL
       for(j=1; j<= nlstate; j++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
         for(h=0; h<=nhstepm; h++){  #else
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        t= t- del*SQR(fp-fptt);
         }  #endif
       }        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
      #ifdef DEBUG
       for(i=1; i<=npar; i++) /* Computes gradient */        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);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        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);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
          fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       if (popbased==1) {               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         for(i=1; i<=nlstate;i++)        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);
           prlim[i][i]=probs[(int)age][i][ij];        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);
       }  #endif
   #ifdef POWELLORIGINAL
       for(j=1; j<= nlstate; j++){        if (t < 0.0) { /* Then we use it for new direction */
         for(h=0; h<=nhstepm; h++){  #else
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        if (directest*t < 0.0) { /* Contradiction between both tests */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
         }        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       }        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       for(j=1; j<= nlstate; j++)      } 
         for(h=0; h<=nhstepm; h++){        if (directest < 0.0) { /* Then we use it for new direction */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  #endif
         }          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
     } /* End theta */          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
           }
     for(h=0; h<=nhstepm; h++)          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
       for(j=1; j<=nlstate;j++)          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++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(i=1;i<=nlstate;i++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for(j=1;j<=nlstate;j++)          for(j=1;j<=n;j++){
         vareij[i][j][(int)age] =0.;            printf(" %.12e",xit[j]);
     for(h=0;h<=nhstepm;h++){            fprintf(ficlog," %.12e",xit[j]);
       for(k=0;k<=nhstepm;k++){          }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          printf("\n");
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          fprintf(ficlog,"\n");
         for(i=1;i<=nlstate;i++)  #endif
           for(j=1;j<=nlstate;j++)        } /* end of t negative */
             vareij[i][j][(int)age] += doldm[i][j];      } /* end if (fptt < fp)  */
       }    } 
     }  } 
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;  /**** Prevalence limit (stable or period prevalence)  ****************/
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       for(j=1; j<=nlstate;j++){  {
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
     fprintf(ficresvij,"\n");    
     free_matrix(gp,0,nhstepm,1,nlstate);    int i, ii,j,k;
     free_matrix(gm,0,nhstepm,1,nlstate);    double min, max, maxmin, maxmax,sumnew=0.;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    /* double **matprod2(); */ /* test */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double **out, cov[NCOVMAX+1], **pmij();
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **newm;
   } /* End age */    double agefin, delaymax=50 ; /* Max number of years to converge */
      
   free_vector(xp,1,npar);    for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(doldm,1,nlstate,1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(dnewm,1,nlstate,1,nlstate);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
 }    
     cov[1]=1.;
 /************ 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)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   /* Variance of prevalence limit */      newm=savm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      /* Covariates have to be included here again */
   double **newm;      cov[2]=agefin;
   double **dnewm,**doldm;      
   int i, j, nhstepm, hstepm;      for (k=1; k<=cptcovn;k++) {
   int k, cptcode;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double *xp;        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
   double *gp, *gm;      }
   double **gradg, **trgradg;      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   double age,agelim;      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
   int theta;      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]]];
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      
   fprintf(ficresvpl,"# Age");      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for(i=1; i<=nlstate;i++)      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       fprintf(ficresvpl," %1d-%1d",i,i);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   fprintf(ficresvpl,"\n");      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   xp=vector(1,npar);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   dnewm=matrix(1,nlstate,1,npar);      
   doldm=matrix(1,nlstate,1,nlstate);      savm=oldm;
        oldm=newm;
   hstepm=1*YEARM; /* Every year of age */      maxmax=0.;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for(j=1;j<=nlstate;j++){
   agelim = AGESUP;        min=1.;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        max=0.;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(i=1; i<=nlstate; i++) {
     if (stepm >= YEARM) hstepm=1;          sumnew=0;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     gradg=matrix(1,npar,1,nlstate);          prlim[i][j]= newm[i][j]/(1-sumnew);
     gp=vector(1,nlstate);          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
     gm=vector(1,nlstate);          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
     for(theta=1; theta <=npar; theta++){        }
       for(i=1; i<=npar; i++){ /* Computes gradient */        maxmin=max-min;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        maxmax=FMAX(maxmax,maxmin);
       }      } /* j loop */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if(maxmax < ftolpl){
       for(i=1;i<=nlstate;i++)        return prlim;
         gp[i] = prlim[i][i];      }
        } /* age loop */
       for(i=1; i<=npar; i++) /* Computes gradient */    return prlim; /* should not reach here */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  /*************** transition probabilities ***************/ 
         gm[i] = prlim[i][i];  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for(i=1;i<=nlstate;i++)  {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    /* According to parameters values stored in x and the covariate's values stored in cov,
     } /* End theta */       computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
     trgradg =matrix(1,nlstate,1,npar);       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     for(j=1; j<=nlstate;j++)       ncth covariate in the global vector x is given by the formula:
       for(theta=1; theta <=npar; theta++)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
         trgradg[j][theta]=gradg[theta][j];       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     for(i=1;i<=nlstate;i++)       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       varpl[i][(int)age] =0.;       Outputs ps[i][j] the probability to be observed in j being in j according to
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    */
     for(i=1;i<=nlstate;i++)    double s1, lnpijopii;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    /*double t34;*/
     int i,j, nc, ii, jj;
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)      for(i=1; i<= nlstate; i++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        for(j=1; j<i;j++){
     fprintf(ficresvpl,"\n");          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     free_vector(gp,1,nlstate);            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     free_vector(gm,1,nlstate);            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     free_matrix(gradg,1,npar,1,nlstate);  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     free_matrix(trgradg,1,nlstate,1,npar);          }
   } /* End age */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   free_vector(xp,1,npar);        }
   free_matrix(doldm,1,nlstate,1,npar);        for(j=i+1; j<=nlstate+ndeath;j++){
   free_matrix(dnewm,1,nlstate,1,nlstate);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
 }            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
 /************ Variance of one-step probabilities  ******************/          }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 {        }
   int i, j;      }
   int k=0, cptcode;      
   double **dnewm,**doldm;      for(i=1; i<= nlstate; i++){
   double *xp;        s1=0;
   double *gp, *gm;        for(j=1; j<i; j++){
   double **gradg, **trgradg;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   double age,agelim, cov[NCOVMAX];          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   int theta;        }
   char fileresprob[FILENAMELENGTH];        for(j=i+1; j<=nlstate+ndeath; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   strcpy(fileresprob,"prob");          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   strcat(fileresprob,fileres);        }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
     printf("Problem with resultfile: %s\n", fileresprob);        ps[i][i]=1./(s1+1.);
   }        /* Computing other pijs */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        for(j=1; j<i; j++)
            ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
   xp=vector(1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      } /* end i */
        
   cov[1]=1;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   for (age=bage; age<=fage; age ++){        for(jj=1; jj<= nlstate+ndeath; jj++){
     cov[2]=age;          ps[ii][jj]=0;
     gradg=matrix(1,npar,1,9);          ps[ii][ii]=1;
     trgradg=matrix(1,9,1,npar);        }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      
          
     for(theta=1; theta <=npar; theta++){      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       for(i=1; i<=npar; i++)      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
            /*   } */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      /*   printf("\n "); */
          /* } */
       k=0;      /* printf("\n ");printf("%lf ",cov[2]);*/
       for(i=1; i<= (nlstate+ndeath); i++){      /*
         for(j=1; j<=(nlstate+ndeath);j++){        for(i=1; i<= npar; i++) printf("%f ",x[i]);
            k=k+1;        goto end;*/
           gp[k]=pmmij[i][j];      return ps;
         }  }
       }  
   /**************** Product of 2 matrices ******************/
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
      {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       pmij(pmmij,cov,ncovmodel,xp,nlstate);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       k=0;    /* in, b, out are matrice of pointers which should have been initialized 
       for(i=1; i<=(nlstate+ndeath); i++){       before: only the contents of out is modified. The function returns
         for(j=1; j<=(nlstate+ndeath);j++){       a pointer to pointers identical to out */
           k=k+1;    int i, j, k;
           gm[k]=pmmij[i][j];    for(i=nrl; i<= nrh; i++)
         }      for(k=ncolol; k<=ncoloh; k++){
       }        out[i][k]=0.;
              for(j=ncl; j<=nch; j++)
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          out[i][k] +=in[i][j]*b[j][k];
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        }
     }    return out;
   }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
       for(theta=1; theta <=npar; theta++)  
       trgradg[j][theta]=gradg[theta][j];  /************* Higher Matrix Product ***************/
    
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  {
     /* Computes the transition matrix starting at age 'age' over 
      pmij(pmmij,cov,ncovmodel,x,nlstate);       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      k=0;       nhstepm*hstepm matrices. 
      for(i=1; i<=(nlstate+ndeath); i++){       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        for(j=1; j<=(nlstate+ndeath);j++){       (typically every 2 years instead of every month which is too big 
          k=k+1;       for the memory).
          gm[k]=pmmij[i][j];       Model is determined by parameters x and covariates have to be 
         }       included manually here. 
      }  
             */
      /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    int i, j, d, h, k;
            double **out, cov[NCOVMAX+1];
     double **newm;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
      }*/    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
   fprintf(ficresprob,"\n%d ",(int)age);      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   }    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        newm=savm;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        /* Covariates have to be included here again */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        cov[1]=1.;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 }        for (k=1; k<=cptcovn;k++) 
  free_vector(xp,1,npar);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 fclose(ficresprob);        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
           /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
 }          cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
 /******************* Printing html file ***********/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){  
   int jj1, k1, i1, cpt;  
   FILE *fichtm;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   /*char optionfilehtm[FILENAMELENGTH];*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   strcpy(optionfilehtm,optionfile);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   strcat(optionfilehtm,".htm");        savm=oldm;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        oldm=newm;
     printf("Problem with %s \n",optionfilehtm), exit(0);      }
   }      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71c </font> <hr size=\"2\" color=\"#EC5E5E\">          po[i][j][h]=newm[i][j];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
 Total number of observations=%d <br>      /*printf("h=%d ",h);*/
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    } /* end h */
 <hr  size=\"2\" color=\"#EC5E5E\">  /*     printf("\n H=%d \n",h); */
 <li>Outputs files<br><br>\n    return po;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  }
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  #ifdef NLOPT
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    double fret;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    double *xt;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    int j;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    myfunc_data *d2 = (myfunc_data *) pd;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  /* xt = (p1-1); */
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    xt=vector(1,n); 
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
      fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
 fprintf(fichtm," <li>Graphs</li><p>");    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     printf("Function = %.12lf ",fret);
  m=cptcoveff;    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    printf("\n");
    free_vector(xt,1,n);
  jj1=0;    return fret;
  for(k1=1; k1<=m;k1++){  }
    for(i1=1; i1<=ncodemax[k1];i1++){  #endif
        jj1++;  
        if (cptcovn > 0) {  /*************** log-likelihood *************/
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  double func( double *x)
          for (cpt=1; cpt<=cptcoveff;cpt++)  {
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    int i, ii, j, k, mi, d, kk;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
        }    double **out;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    double sw; /* Sum of weights */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        double lli; /* Individual log likelihood */
        for(cpt=1; cpt<nlstate;cpt++){    int s1, s2;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    double bbh, survp;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    long ipmx;
        }    /*extern weight */
     for(cpt=1; cpt<=nlstate;cpt++) {    /* We are differentiating ll according to initial status */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 interval) in state (%d): v%s%d%d.gif <br>    /*for(i=1;i<imx;i++) 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        printf(" %d\n",s[4][i]);
      }    */
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    ++countcallfunc;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }    cov[1]=1.;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.gif<br>    for(k=1; k<=nlstate; k++) ll[k]=0.;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
 fprintf(fichtm,"\n</body>");    if(mle==1){
    }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    }        /* Computes the values of the ncovmodel covariates of the model
 fclose(fichtm);           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
 }           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
            to be observed in j being in i according to the model.
 /******************* Gnuplot file **************/         */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
           cov[2+k]=covar[Tvar[k]][i];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        }
         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   strcpy(optionfilegnuplot,optionfilefiname);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   strcat(optionfilegnuplot,".plt");           has been calculated etc */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        for(mi=1; mi<= wav[i]-1; mi++){
     printf("Problem with file %s",optionfilegnuplot);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef windows              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficgp,"cd \"%s\" \n",pathc);            }
 #endif          for(d=0; d<dh[mi][i]; d++){
 m=pow(2,cptcoveff);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  /* 1eme*/            for (kk=1; kk<=cptcovage;kk++) {
   for (cpt=1; cpt<= nlstate ; cpt ++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
    for (k1=1; k1<= m ; k1 ++) {            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #ifdef windows                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     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);            savm=oldm;
 #endif            oldm=newm;
 #ifdef unix          } /* end mult */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        
 #endif          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
 for (i=1; i<= nlstate ; i ++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           * (in months) between two waves is not a multiple of stepm, we rounded to 
   else fprintf(ficgp," \%%*lf (\%%*lf)");           * the nearest (and in case of equal distance, to the lowest) interval but now
 }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     for (i=1; i<= nlstate ; i ++) {           * probability in order to take into account the bias as a fraction of the way
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   else fprintf(ficgp," \%%*lf (\%%*lf)");           * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);           * For stepm > 1 the results are less biased than in previous versions. 
      for (i=1; i<= nlstate ; i ++) {           */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          s1=s[mw[mi][i]][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          s2=s[mw[mi+1][i]][i];
 }            bbh=(double)bh[mi][i]/(double)stepm; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          /* bias bh is positive if real duration
 #ifdef unix           * is higher than the multiple of stepm and negative otherwise.
 fprintf(ficgp,"\nset ter gif small size 400,300");           */
 #endif          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          if( s2 > nlstate){ 
    }            /* i.e. if s2 is a death state and if the date of death is known 
   }               then the contribution to the likelihood is the probability to 
   /*2 eme*/               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
   for (k1=1; k1<= m ; k1 ++) {               minus probability to die before dh-stepm . 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);               In version up to 0.92 likelihood was computed
              as if date of death was unknown. Death was treated as any other
     for (i=1; i<= nlstate+1 ; i ++) {          health state: the date of the interview describes the actual state
       k=2*i;          and not the date of a change in health state. The former idea was
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          to consider that at each interview the state was recorded
       for (j=1; j<= nlstate+1 ; j ++) {          (healthy, disable or death) and IMaCh was corrected; but when we
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          introduced the exact date of death then we should have modified
   else fprintf(ficgp," \%%*lf (\%%*lf)");          the contribution of an exact death to the likelihood. This new
 }            contribution is smaller and very dependent of the step unit
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          stepm. It is no more the probability to die between last interview
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          and month of death but the probability to survive from last
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          interview up to one month before death multiplied by the
       for (j=1; j<= nlstate+1 ; j ++) {          probability to die within a month. Thanks to Chris
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          Jackson for correcting this bug.  Former versions increased
         else fprintf(ficgp," \%%*lf (\%%*lf)");          mortality artificially. The bad side is that we add another loop
 }            which slows down the processing. The difference can be up to 10%
       fprintf(ficgp,"\" t\"\" w l 0,");          lower mortality.
      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 ++) {          /* If, at the beginning of the maximization mostly, the
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");             cumulative probability or probability to be dead is
   else fprintf(ficgp," \%%*lf (\%%*lf)");             constant (ie = 1) over time d, the difference is equal to
 }               0.  out[s1][3] = savm[s1][3]: probability, being at state
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");             s1 at precedent wave, to be dead a month before current
       else fprintf(ficgp,"\" t\"\" w l 0,");             wave is equal to probability, being at state s1 at
     }             precedent wave, to be dead at mont of the current
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);             wave. Then the observed probability (that this person died)
   }             is null according to current estimated parameter. In fact,
               it should be very low but not zero otherwise the log go to
   /*3eme*/             infinity.
           */
   for (k1=1; k1<= m ; k1 ++) {  /* #ifdef INFINITYORIGINAL */
     for (cpt=1; cpt<= nlstate ; cpt ++) {  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
       k=2+nlstate*(cpt-1);  /* #else */
       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);  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
       for (i=1; i< nlstate ; i ++) {  /*          lli=log(mytinydouble); */
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);  /*        else */
       }  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  /* #endif */
     }              lli=log(out[s1][s2] - savm[s1][s2]);
     }  
            } else if  (s2==-2) {
   /* CV preval stat */            for (j=1,survp=0. ; j<=nlstate; j++) 
     for (k1=1; k1<= m ; k1 ++) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for (cpt=1; cpt<nlstate ; cpt ++) {            /*survp += out[s1][j]; */
       k=3;            lli= log(survp);
       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,agemaxpar,fileres,k1,k+cpt+1,k+1);          }
           
       for (i=1; i< nlstate ; i ++)          else if  (s2==-4) { 
         fprintf(ficgp,"+$%d",k+i+1);            for (j=3,survp=0. ; j<=nlstate; j++)  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                  lli= log(survp); 
       l=3+(nlstate+ndeath)*cpt;          } 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {          else if  (s2==-5) { 
         l=3+(nlstate+ndeath)*cpt;            for (j=1,survp=0. ; j<=2; j++)  
         fprintf(ficgp,"+$%d",l+i+1);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            } 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          
     }          else{
   }              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
              /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   /* proba elementaires */          } 
    for(i=1,jk=1; i <=nlstate; i++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     for(k=1; k <=(nlstate+ndeath); k++){          /*if(lli ==000.0)*/
       if (k != i) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         for(j=1; j <=ncovmodel; j++){          ipmx +=1;
                  sw += weight[i];
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           jk++;          /* if (lli < log(mytinydouble)){ */
           fprintf(ficgp,"\n");          /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
         }          /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
       }          /* } */
     }        } /* end of wave */
     }      } /* end of individual */
     }  else if(mle==2){
     for(jk=1; jk <=m; jk++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
    i=1;        for(mi=1; mi<= wav[i]-1; mi++){
    for(k2=1; k2<=nlstate; k2++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
      k3=i;            for (j=1;j<=nlstate+ndeath;j++){
      for(k=1; k<=(nlstate+ndeath); k++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        if (k != k2){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            }
 ij=1;          for(d=0; d<=dh[mi][i]; d++){
         for(j=3; j <=ncovmodel; j++) {            newm=savm;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            for (kk=1; kk<=cptcovage;kk++) {
             ij++;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }            }
           else            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
           fprintf(ficgp,")/(1");            oldm=newm;
                  } /* end mult */
         for(k1=1; k1 <=nlstate; k1++){          
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          s1=s[mw[mi][i]][i];
 ij=1;          s2=s[mw[mi+1][i]][i];
           for(j=3; j <=ncovmodel; j++){          bbh=(double)bh[mi][i]/(double)stepm; 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          ipmx +=1;
             ij++;          sw += weight[i];
           }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           else        } /* end of wave */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      } /* end of individual */
           }    }  else if(mle==3){  /* exponential inter-extrapolation */
           fprintf(ficgp,")");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for(mi=1; mi<= wav[i]-1; mi++){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          for (ii=1;ii<=nlstate+ndeath;ii++)
         i=i+ncovmodel;            for (j=1;j<=nlstate+ndeath;j++){
        }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    }            }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          for(d=0; d<dh[mi][i]; d++){
    }            newm=savm;
                cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fclose(ficgp);            for (kk=1; kk<=cptcovage;kk++) {
 }  /* end gnuplot */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /*************** Moving average **************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){            savm=oldm;
             oldm=newm;
   int i, cpt, cptcod;          } /* end mult */
     for (agedeb=agemin; agedeb<=fage; agedeb++)        
       for (i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          s2=s[mw[mi+1][i]][i];
           mobaverage[(int)agedeb][i][cptcod]=0.;          bbh=(double)bh[mi][i]/(double)stepm; 
              lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){          ipmx +=1;
       for (i=1; i<=nlstate;i++){          sw += weight[i];
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for (cpt=0;cpt<=4;cpt++){        } /* end of wave */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      } /* end of individual */
           }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
                for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 /************** Forecasting ******************/          for(d=0; d<dh[mi][i]; d++){
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            for (kk=1; kk<=cptcovage;kk++) {
   int *popage;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            }
   double *popeffectif,*popcount;          
   double ***p3mat;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   char fileresf[FILENAMELENGTH];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
  agelim=AGESUP;            oldm=newm;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          } /* end mult */
         
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
            if( s2 > nlstate){ 
   strcpy(fileresf,"f");            lli=log(out[s1][s2] - savm[s1][s2]);
   strcat(fileresf,fileres);          }else{
   if((ficresf=fopen(fileresf,"w"))==NULL) {            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     printf("Problem with forecast resultfile: %s\n", fileresf);          }
   }          ipmx +=1;
   printf("Computing forecasting: result on file '%s' \n", fileresf);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
   if (mobilav==1) {      } /* end of individual */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     movingaverage(agedeb, fage, agemin, mobaverage);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for (ii=1;ii<=nlstate+ndeath;ii++)
   if (stepm<=12) stepsize=1;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   agelim=AGESUP;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   hstepm=1;          for(d=0; d<dh[mi][i]; d++){
   hstepm=hstepm/stepm;            newm=savm;
   yp1=modf(dateintmean,&yp);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   anprojmean=yp;            for (kk=1; kk<=cptcovage;kk++) {
   yp2=modf((yp1*12),&yp);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   mprojmean=yp;            }
   yp1=modf((yp2*30.5),&yp);          
   jprojmean=yp;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if(jprojmean==0) jprojmean=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if(mprojmean==0) jprojmean=1;            savm=oldm;
              oldm=newm;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          } /* end mult */
          
   for(cptcov=1;cptcov<=i2;cptcov++){          s1=s[mw[mi][i]][i];
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          s2=s[mw[mi+1][i]][i];
       k=k+1;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficresf,"\n#******");          ipmx +=1;
       for(j=1;j<=cptcoveff;j++) {          sw += weight[i];
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          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]);*/
       fprintf(ficresf,"******\n");        } /* end of wave */
       fprintf(ficresf,"# StartingAge FinalAge");      } /* end of individual */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    } /* End of if */
          for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
          /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         fprintf(ficresf,"\n");    return -l;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    }
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  /*************** log-likelihood *************/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  double funcone( double *x)
           nhstepm = nhstepm/hstepm;  {
              /* Same as likeli but slower because of a lot of printf and if */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i, ii, j, k, mi, d, kk;
           oldm=oldms;savm=savms;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double **out;
            double lli; /* Individual log likelihood */
           for (h=0; h<=nhstepm; h++){    double llt;
             if (h==(int) (calagedate+YEARM*cpt)) {    int s1, s2;
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    double bbh, survp;
             }    /*extern weight */
             for(j=1; j<=nlstate+ndeath;j++) {    /* We are differentiating ll according to initial status */
               kk1=0.;kk2=0;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
               for(i=1; i<=nlstate;i++) {                  /*for(i=1;i<imx;i++) 
                 if (mobilav==1)      printf(" %d\n",s[4][i]);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    */
                 else {    cov[1]=1.;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }    for(k=1; k<=nlstate; k++) ll[k]=0.;
                  
               }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               if (h==(int)(calagedate+12*cpt)){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                 fprintf(ficresf," %.3f", kk1);      for(mi=1; mi<= wav[i]-1; mi++){
                                for (ii=1;ii<=nlstate+ndeath;ii++)
               }          for (j=1;j<=nlstate+ndeath;j++){
             }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
         }        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];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   fclose(ficresf);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /************** Forecasting ******************/          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
            savm=oldm;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          oldm=newm;
   int *popage;        } /* end mult */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        
   double *popeffectif,*popcount;        s1=s[mw[mi][i]][i];
   double ***p3mat,***tabpop,***tabpopprev;        s2=s[mw[mi+1][i]][i];
   char filerespop[FILENAMELENGTH];        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         * is higher than the multiple of stepm and negative otherwise.
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         */
   agelim=AGESUP;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          lli=log(out[s1][s2] - savm[s1][s2]);
          } else if  (s2==-2) {
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          for (j=1,survp=0. ; j<=nlstate; j++) 
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
   strcpy(filerespop,"pop");        }else if (mle==1){
   strcat(filerespop,fileres);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        } else if(mle==2){
     printf("Problem with forecast resultfile: %s\n", filerespop);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   }        } else if(mle==3){  /* exponential inter-extrapolation */
   printf("Computing forecasting: result on file '%s' \n", filerespop);          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
   if (mobilav==1) {          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          /*lli=log(out[s1][s2]); */ /* Original formula */
     movingaverage(agedeb, fage, agemin, mobaverage);        } /* End of if */
   }        ipmx +=1;
         sw += weight[i];
   stepsize=(int) (stepm+YEARM-1)/YEARM;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if (stepm<=12) stepsize=1;        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
          if(globpr){
   agelim=AGESUP;          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     %11.6f %11.6f %11.6f ", \
   hstepm=1;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   hstepm=hstepm/stepm;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   if (popforecast==1) {            llt +=ll[k]*gipmx/gsw;
     if((ficpop=fopen(popfile,"r"))==NULL) {            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       printf("Problem with population file : %s\n",popfile);exit(0);          }
     }          fprintf(ficresilk," %10.6f\n", -llt);
     popage=ivector(0,AGESUP);        }
     popeffectif=vector(0,AGESUP);      } /* end of wave */
     popcount=vector(0,AGESUP);    } /* end of individual */
        for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     i=1;      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
        if(globpr==0){ /* First time we count the contributions and weights */
     imx=i;      gipmx=ipmx;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      gsw=sw;
   }    }
     return -l;
   for(cptcov=1;cptcov<=i2;cptcov++){  }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;  
       fprintf(ficrespop,"\n#******");  /*************** function likelione ***********/
       for(j=1;j<=cptcoveff;j++) {  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  {
       }    /* This routine should help understanding what is done with 
       fprintf(ficrespop,"******\n");       the selection of individuals/waves and
       fprintf(ficrespop,"# Age");       to check the exact contribution to the likelihood.
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);       Plotting could be done.
       if (popforecast==1)  fprintf(ficrespop," [Population]");     */
          int k;
       for (cpt=0; cpt<=0;cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      if(*globpri !=0){ /* Just counts and sums, no printings */
              strcpy(fileresilk,"ilk"); 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      strcat(fileresilk,fileres);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
           nhstepm = nhstepm/hstepm;        printf("Problem with resultfile: %s\n", fileresilk);
                  fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
           oldm=oldms;savm=savms;      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");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        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]); */
           for (h=0; h<=nhstepm; h++){      for(k=1; k<=nlstate; k++) 
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
             }    }
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    *fretone=(*funcone)(p);
               for(i=1; i<=nlstate;i++) {                  if(*globpri !=0){
                 if (mobilav==1)      fclose(ficresilk);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
                 else {      fflush(fichtm); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    } 
                 }    return;
               }  }
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);  /*********** Maximum Likelihood Estimation ***************/
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
             }  {
             for(i=1; i<=nlstate;i++){    int i,j, iter=0;
               kk1=0.;    double **xi;
                 for(j=1; j<=nlstate;j++){    double fret;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    double fretone; /* Only one call to likelihood */
                 }    /*  char filerespow[FILENAMELENGTH];*/
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  
             }  #ifdef NLOPT
     int creturn;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    nlopt_opt opt;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
           }    double *lb;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double minf; /* the minimum objective value, upon return */
         }    double * p1; /* Shifted parameters from 0 instead of 1 */
       }    myfunc_data dinst, *d = &dinst;
    #endif
   /******/  
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    xi=matrix(1,npar,1,npar);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      for (i=1;i<=npar;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      for (j=1;j<=npar;j++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        xi[i][j]=(i==j ? 1.0 : 0.0);
           nhstepm = nhstepm/hstepm;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
              strcpy(filerespow,"pow"); 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(filerespow,fileres);
           oldm=oldms;savm=savms;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        printf("Problem with resultfile: %s\n", filerespow);
           for (h=0; h<=nhstepm; h++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
             if (h==(int) (calagedate+YEARM*cpt)) {    }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
             }    for (i=1;i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++) {      for(j=1;j<=nlstate+ndeath;j++)
               kk1=0.;kk2=0;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
               for(i=1; i<=nlstate;i++) {                  fprintf(ficrespow,"\n");
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      #ifdef POWELL
               }    powell(p,xi,npar,ftol,&iter,&fret,func);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  #endif
             }  
           }  #ifdef NLOPT
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #ifdef NEWUOA
         }    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
       }  #else
    }    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   }  #endif
      lb=vector(0,npar-1);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     nlopt_set_lower_bounds(opt, lb);
   if (popforecast==1) {    nlopt_set_initial_step1(opt, 0.1);
     free_ivector(popage,0,AGESUP);    
     free_vector(popeffectif,0,AGESUP);    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     free_vector(popcount,0,AGESUP);    d->function = func;
   }    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    nlopt_set_min_objective(opt, myfunc, d);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    nlopt_set_xtol_rel(opt, ftol);
   fclose(ficrespop);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
 }      printf("nlopt failed! %d\n",creturn); 
     }
 /***********************************************/    else {
 /**************** Main Program *****************/      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
 /***********************************************/      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
 int main(int argc, char *argv[])    }
 {    nlopt_destroy(opt);
   #endif
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    free_matrix(xi,1,npar,1,npar);
   double agedeb, agefin,hf;    fclose(ficrespow);
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    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));
   double fret;    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   double **xi,tmp,delta;  
   }
   double dum; /* Dummy variable */  
   double ***p3mat;  /**** Computes Hessian and covariance matrix ***/
   int *indx;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   char line[MAXLINE], linepar[MAXLINE];  {
   char title[MAXLINE];    double  **a,**y,*x,pd;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    double **hess;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    int i, j;
      int *indx;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   char filerest[FILENAMELENGTH];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   char fileregp[FILENAMELENGTH];    void lubksb(double **a, int npar, int *indx, double b[]) ;
   char popfile[FILENAMELENGTH];    void ludcmp(double **a, int npar, int *indx, double *d) ;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    double gompertz(double p[]);
   int firstobs=1, lastobs=10;    hess=matrix(1,npar,1,npar);
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;    printf("\nCalculation of the hessian matrix. Wait...\n");
   int ju,jl, mi;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    for (i=1;i<=npar;i++){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      printf("%d",i);fflush(stdout);
   int mobilav=0,popforecast=0;      fprintf(ficlog,"%d",i);fflush(ficlog);
   int hstepm, nhstepm;     
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
   double bage, fage, age, agelim, agebase;      /*  printf(" %f ",p[i]);
   double ftolpl=FTOL;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   double **prlim;    }
   double *severity;    
   double ***param; /* Matrix of parameters */    for (i=1;i<=npar;i++) {
   double  *p;      for (j=1;j<=npar;j++)  {
   double **matcov; /* Matrix of covariance */        if (j>i) { 
   double ***delti3; /* Scale */          printf(".%d%d",i,j);fflush(stdout);
   double *delti; /* Scale */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double ***eij, ***vareij;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   double **varpl; /* Variances of prevalence limits by age */          
   double *epj, vepp;          hess[j][i]=hess[i][j];    
   double kk1, kk2;          /*printf(" %lf ",hess[i][j]);*/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        }
        }
     }
   char version[80]="Imach version 0.71c, March 2002, INED-EUROREVES ";    printf("\n");
   char *alph[]={"a","a","b","c","d","e"}, str[4];    fprintf(ficlog,"\n");
   
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   char z[1]="c", occ;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 #include <sys/time.h>    
 #include <time.h>    a=matrix(1,npar,1,npar);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    y=matrix(1,npar,1,npar);
      x=vector(1,npar);
   /* long total_usecs;    indx=ivector(1,npar);
   struct timeval start_time, end_time;    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    ludcmp(a,npar,indx,&pd);
   
     for (j=1;j<=npar;j++) {
   printf("\n%s",version);      for (i=1;i<=npar;i++) x[i]=0;
   if(argc <=1){      x[j]=1;
     printf("\nEnter the parameter file name: ");      lubksb(a,npar,indx,x);
     scanf("%s",pathtot);      for (i=1;i<=npar;i++){ 
   }        matcov[i][j]=x[i];
   else{      }
     strcpy(pathtot,argv[1]);    }
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    printf("\n#Hessian matrix#\n");
   /*cygwin_split_path(pathtot,path,optionfile);    fprintf(ficlog,"\n#Hessian matrix#\n");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for (i=1;i<=npar;i++) { 
   /* cutv(path,optionfile,pathtot,'\\');*/      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        fprintf(ficlog,"%.3e ",hess[i][j]);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      }
   chdir(path);      printf("\n");
   replace(pathc,path);      fprintf(ficlog,"\n");
     }
 /*-------- arguments in the command line --------*/  
     /* Recompute Inverse */
   strcpy(fileres,"r");    for (i=1;i<=npar;i++)
   strcat(fileres, optionfilefiname);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   strcat(fileres,".txt");    /* Other files have txt extension */    ludcmp(a,npar,indx,&pd);
   
   /*---------arguments file --------*/    /*  printf("\n#Hessian matrix recomputed#\n");
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    for (j=1;j<=npar;j++) {
     printf("Problem with optionfile %s\n",optionfile);      for (i=1;i<=npar;i++) x[i]=0;
     goto end;      x[j]=1;
   }      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   strcpy(filereso,"o");        y[i][j]=x[i];
   strcat(filereso,fileres);        printf("%.3e ",y[i][j]);
   if((ficparo=fopen(filereso,"w"))==NULL) {        fprintf(ficlog,"%.3e ",y[i][j]);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      }
   }      printf("\n");
       fprintf(ficlog,"\n");
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    free_matrix(a,1,npar,1,npar);
     puts(line);    free_matrix(y,1,npar,1,npar);
     fputs(line,ficparo);    free_vector(x,1,npar);
   }    free_ivector(indx,1,npar);
   ungetc(c,ficpar);    free_matrix(hess,1,npar,1,npar);
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);  }
   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){  /*************** hessian matrix ****************/
     ungetc(c,ficpar);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    int i;
     fputs(line,ficparo);    int l=1, lmax=20;
   }    double k1,k2;
   ungetc(c,ficpar);    double p2[MAXPARM+1]; /* identical to x */
      double res;
        double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   covar=matrix(0,NCOVMAX,1,n);    double fx;
   cptcovn=0;    int k=0,kmax=10;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    double l1;
   
   ncovmodel=2+cptcovn;    fx=func(x);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    for (i=1;i<=npar;i++) p2[i]=x[i];
      for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
   /* Read guess parameters */      l1=pow(10,l);
   /* Reads comments: lines beginning with '#' */      delts=delt;
   while((c=getc(ficpar))=='#' && c!= EOF){      for(k=1 ; k <kmax; k=k+1){
     ungetc(c,ficpar);        delt = delta*(l1*k);
     fgets(line, MAXLINE, ficpar);        p2[theta]=x[theta] +delt;
     puts(line);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
     fputs(line,ficparo);        p2[theta]=x[theta]-delt;
   }        k2=func(p2)-fx;
   ungetc(c,ficpar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        
     for(i=1; i <=nlstate; i++)  #ifdef DEBUGHESS
     for(j=1; j <=nlstate+ndeath-1; j++){        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fscanf(ficpar,"%1d%1d",&i1,&j1);        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);
       fprintf(ficparo,"%1d%1d",i1,j1);  #endif
       printf("%1d%1d",i,j);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for(k=1; k<=ncovmodel;k++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         fscanf(ficpar," %lf",&param[i][j][k]);          k=kmax;
         printf(" %lf",param[i][j][k]);        }
         fprintf(ficparo," %lf",param[i][j][k]);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       }          k=kmax; l=lmax*10;
       fscanf(ficpar,"\n");        }
       printf("\n");        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       fprintf(ficparo,"\n");          delts=delt;
     }        }
        }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    }
     delti[theta]=delts;
   p=param[1][1];    return res; 
      
   /* Reads comments: lines beginning with '#' */  }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    int i;
     fputs(line,ficparo);    int l=1, lmax=20;
   }    double k1,k2,k3,k4,res,fx;
   ungetc(c,ficpar);    double p2[MAXPARM+1];
     int k;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fx=func(x);
   for(i=1; i <=nlstate; i++){    for (k=1; k<=2; k++) {
     for(j=1; j <=nlstate+ndeath-1; j++){      for (i=1;i<=npar;i++) p2[i]=x[i];
       fscanf(ficpar,"%1d%1d",&i1,&j1);      p2[thetai]=x[thetai]+delti[thetai]/k;
       printf("%1d%1d",i,j);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fprintf(ficparo,"%1d%1d",i1,j1);      k1=func(p2)-fx;
       for(k=1; k<=ncovmodel;k++){    
         fscanf(ficpar,"%le",&delti3[i][j][k]);      p2[thetai]=x[thetai]+delti[thetai]/k;
         printf(" %le",delti3[i][j][k]);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         fprintf(ficparo," %le",delti3[i][j][k]);      k2=func(p2)-fx;
       }    
       fscanf(ficpar,"\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
       printf("\n");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fprintf(ficparo,"\n");      k3=func(p2)-fx;
     }    
   }      p2[thetai]=x[thetai]-delti[thetai]/k;
   delti=delti3[1][1];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k4=func(p2)-fx;
   /* Reads comments: lines beginning with '#' */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   while((c=getc(ficpar))=='#' && c!= EOF){  #ifdef DEBUG
     ungetc(c,ficpar);      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);
     fgets(line, MAXLINE, ficpar);      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);
     puts(line);  #endif
     fputs(line,ficparo);    }
   }    return res;
   ungetc(c,ficpar);  }
    
   matcov=matrix(1,npar,1,npar);  /************** Inverse of matrix **************/
   for(i=1; i <=npar; i++){  void ludcmp(double **a, int n, int *indx, double *d) 
     fscanf(ficpar,"%s",&str);  { 
     printf("%s",str);    int i,imax,j,k; 
     fprintf(ficparo,"%s",str);    double big,dum,sum,temp; 
     for(j=1; j <=i; j++){    double *vv; 
       fscanf(ficpar," %le",&matcov[i][j]);   
       printf(" %.5le",matcov[i][j]);    vv=vector(1,n); 
       fprintf(ficparo," %.5le",matcov[i][j]);    *d=1.0; 
     }    for (i=1;i<=n;i++) { 
     fscanf(ficpar,"\n");      big=0.0; 
     printf("\n");      for (j=1;j<=n;j++) 
     fprintf(ficparo,"\n");        if ((temp=fabs(a[i][j])) > big) big=temp; 
   }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   for(i=1; i <=npar; i++)      vv[i]=1.0/big; 
     for(j=i+1;j<=npar;j++)    } 
       matcov[i][j]=matcov[j][i];    for (j=1;j<=n;j++) { 
          for (i=1;i<j;i++) { 
   printf("\n");        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
     /*-------- Rewriting paramater file ----------*/      } 
      strcpy(rfileres,"r");    /* "Rparameterfile */      big=0.0; 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      for (i=j;i<=n;i++) { 
      strcat(rfileres,".");    /* */        sum=a[i][j]; 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        for (k=1;k<j;k++) 
     if((ficres =fopen(rfileres,"w"))==NULL) {          sum -= a[i][k]*a[k][j]; 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        a[i][j]=sum; 
     }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     fprintf(ficres,"#%s\n",version);          big=dum; 
              imax=i; 
     /*-------- data file ----------*/        } 
     if((fic=fopen(datafile,"r"))==NULL)    {      } 
       printf("Problem with datafile: %s\n", datafile);goto end;      if (j != imax) { 
     }        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
     n= lastobs;          a[imax][k]=a[j][k]; 
     severity = vector(1,maxwav);          a[j][k]=dum; 
     outcome=imatrix(1,maxwav+1,1,n);        } 
     num=ivector(1,n);        *d = -(*d); 
     moisnais=vector(1,n);        vv[imax]=vv[j]; 
     annais=vector(1,n);      } 
     moisdc=vector(1,n);      indx[j]=imax; 
     andc=vector(1,n);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     agedc=vector(1,n);      if (j != n) { 
     cod=ivector(1,n);        dum=1.0/(a[j][j]); 
     weight=vector(1,n);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     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);    free_vector(vv,1,n);  /* Doesn't work */
     s=imatrix(1,maxwav+1,1,n);  ;
     adl=imatrix(1,maxwav+1,1,n);      } 
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
     i=1;    int i,ii=0,ip,j; 
     while (fgets(line, MAXLINE, fic) != NULL)    {    double sum; 
       if ((i >= firstobs) && (i <=lastobs)) {   
            for (i=1;i<=n;i++) { 
         for (j=maxwav;j>=1;j--){      ip=indx[i]; 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      sum=b[ip]; 
           strcpy(line,stra);      b[ip]=b[i]; 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      if (ii) 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         }      else if (sum) ii=i; 
              b[i]=sum; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    } 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    for (i=n;i>=1;i--) { 
       sum=b[i]; 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      b[i]=sum/a[i][i]; 
     } 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  } 
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  void pstamp(FILE *fichier)
         }  {
         num[i]=atol(stra);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
          }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
         i=i+1;  {  /* Some frequencies */
       }    
     }    int i, m, jk, j1, bool, z1,j;
     /* printf("ii=%d", ij);    int first;
        scanf("%d",i);*/    double ***freq; /* Frequencies */
   imx=i-1; /* Number of individuals */    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
   /* for (i=1; i<=imx; i++){    char fileresp[FILENAMELENGTH];
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    pp=vector(1,nlstate);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    prop=matrix(1,nlstate,iagemin,iagemax+3);
     }    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
     for (i=1; i<=imx; i++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   /* Calculation of the number of parameter from char model*/      exit(0);
   Tvar=ivector(1,15);    }
   Tprod=ivector(1,15);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   Tvaraff=ivector(1,15);    j1=0;
   Tvard=imatrix(1,15,1,2);    
   Tage=ivector(1,15);          j=cptcoveff;
        if (cptcovn<1) {j=1;ncodemax[1]=1;}
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;    first=1;
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
     cptcovn=j+1;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
     cptcovprod=j1;    /*    j1++; */
        for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
            /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     strcpy(modelsav,model);          scanf("%d", i);*/
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        for (i=-5; i<=nlstate+ndeath; i++)  
       printf("Error. Non available option model=%s ",model);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       goto end;            for(m=iagemin; m <= iagemax+3; m++)
     }              freq[i][jk][m]=0;
            
     for(i=(j+1); i>=1;i--){        for (i=1; i<=nlstate; i++)  
       cutv(stra,strb,modelsav,'+');          for(m=iagemin; m <= iagemax+3; m++)
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);            prop[i][m]=0;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        
       /*scanf("%d",i);*/        dateintsum=0;
       if (strchr(strb,'*')) {        k2cpt=0;
         cutv(strd,strc,strb,'*');        for (i=1; i<=imx; i++) {
         if (strcmp(strc,"age")==0) {          bool=1;
           cptcovprod--;          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           cutv(strb,stre,strd,'V');            for (z1=1; z1<=cptcoveff; z1++)       
           Tvar[i]=atoi(stre);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
           cptcovage++;                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
             Tage[cptcovage]=i;                bool=0;
             /*printf("stre=%s ", stre);*/                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
         }                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
         else if (strcmp(strd,"age")==0) {                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
           cptcovprod--;                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
           cutv(strb,stre,strc,'V');              } 
           Tvar[i]=atoi(stre);          }
           cptcovage++;   
           Tage[cptcovage]=i;          if (bool==1){
         }            for(m=firstpass; m<=lastpass; m++){
         else {              k2=anint[m][i]+(mint[m][i]/12.);
           cutv(strb,stre,strc,'V');              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
           Tvar[i]=ncov+k1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           cutv(strb,strc,strd,'V');                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           Tprod[k1]=i;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
           Tvard[k1][1]=atoi(strc);                if (m<lastpass) {
           Tvard[k1][2]=atoi(stre);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           Tvar[cptcovn+k2]=Tvard[k1][1];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                }
           for (k=1; k<=lastobs;k++)                
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           k1++;                  dateintsum=dateintsum+k2;
           k2=k2+2;                  k2cpt++;
         }                }
       }                /*}*/
       else {            }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          }
        /*  scanf("%d",i);*/        } /* end i */
       cutv(strd,strc,strb,'V');         
       Tvar[i]=atoi(strc);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       }        pstamp(ficresp);
       strcpy(modelsav,stra);          if  (cptcovn>0) {
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          fprintf(ficresp, "\n#********** Variable "); 
         scanf("%d",i);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresp, "**********\n#");
 }          fprintf(ficlog, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          fprintf(ficlog, "**********\n#");
   printf("cptcovprod=%d ", cptcovprod);        }
   scanf("%d ",i);*/        for(i=1; i<=nlstate;i++) 
     fclose(fic);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
     /*  if(mle==1){*/        
     if (weightopt != 1) { /* Maximisation without weights*/        for(i=iagemin; i <= iagemax+3; i++){
       for(i=1;i<=n;i++) weight[i]=1.0;          if(i==iagemax+3){
     }            fprintf(ficlog,"Total");
     /*-calculation of age at interview from date of interview and age at death -*/          }else{
     agev=matrix(1,maxwav,1,imx);            if(first==1){
               first=0;
    for (i=1; i<=imx; i++)              printf("See log file for details...\n");
      for(m=2; (m<= maxwav); m++)            }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            fprintf(ficlog,"Age %d", i);
          anint[m][i]=9999;          }
          s[m][i]=-1;          for(jk=1; jk <=nlstate ; jk++){
        }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                  pp[jk] += freq[jk][m][i]; 
     for (i=1; i<=imx; i++)  {          }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          for(jk=1; jk <=nlstate ; jk++){
       for(m=1; (m<= maxwav); m++){            for(m=-1, pos=0; m <=0 ; m++)
         if(s[m][i] >0){              pos += freq[jk][m][i];
           if (s[m][i] == nlstate+1) {            if(pp[jk]>=1.e-10){
             if(agedc[i]>0)              if(first==1){
               if(moisdc[i]!=99 && andc[i]!=9999)                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               agev[m][i]=agedc[i];              }
             else {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               if (andc[i]!=9999){            }else{
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              if(first==1)
               agev[m][i]=-1;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }            }
           }          }
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for(jk=1; jk <=nlstate ; jk++){
             if(mint[m][i]==99 || anint[m][i]==9999)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               agev[m][i]=1;              pp[jk] += freq[jk][m][i];
             else if(agev[m][i] <agemin){          }       
               agemin=agev[m][i];          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/            pos += pp[jk];
             }            posprop += prop[jk][i];
             else if(agev[m][i] >agemax){          }
               agemax=agev[m][i];          for(jk=1; jk <=nlstate ; jk++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            if(pos>=1.e-5){
             }              if(first==1)
             /*agev[m][i]=anint[m][i]-annais[i];*/                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             /*   agev[m][i] = age[i]+2*m;*/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           }            }else{
           else { /* =9 */              if(first==1)
             agev[m][i]=1;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             s[m][i]=-1;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           }            }
         }            if( i <= iagemax){
         else /*= 0 Unknown */              if(pos>=1.e-5){
           agev[m][i]=1;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       }                /*probs[i][jk][j1]= pp[jk]/pos;*/
                    /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     }              }
     for (i=1; i<=imx; i++)  {              else
       for(m=1; (m<= maxwav); m++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         if (s[m][i] > (nlstate+ndeath)) {            }
           printf("Error: Wrong value in nlstate or ndeath\n");            }
           goto end;          
         }          for(jk=-1; jk <=nlstate+ndeath; jk++)
       }            for(m=-1; m <=nlstate+ndeath; m++)
     }              if(freq[jk][m][i] !=0 ) {
               if(first==1)
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     free_vector(severity,1,maxwav);              }
     free_imatrix(outcome,1,maxwav+1,1,n);          if(i <= iagemax)
     free_vector(moisnais,1,n);            fprintf(ficresp,"\n");
     free_vector(annais,1,n);          if(first==1)
     /* free_matrix(mint,1,maxwav,1,n);            printf("Others in log...\n");
        free_matrix(anint,1,maxwav,1,n);*/          fprintf(ficlog,"\n");
     free_vector(moisdc,1,n);        }
     free_vector(andc,1,n);        /*}*/
     }
        dateintmean=dateintsum/k2cpt; 
     wav=ivector(1,imx);   
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    fclose(ficresp);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
        free_vector(pp,1,nlstate);
     /* Concatenates waves */    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    /* End of Freq */
   }
   
       Tcode=ivector(1,100);  /************ Prevalence ********************/
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  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)
       ncodemax[1]=1;  {  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
             in each health status at the date of interview (if between dateprev1 and dateprev2).
    codtab=imatrix(1,100,1,10);       We still use firstpass and lastpass as another selection.
    h=0;    */
    m=pow(2,cptcoveff);   
      int i, m, jk, j1, bool, z1,j;
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    double **prop;
        for(j=1; j <= ncodemax[k]; j++){    double posprop; 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    double  y2; /* in fractional years */
            h++;    int iagemin, iagemax;
            if (h>m) h=1;codtab[h][k]=j;    int first; /** to stop verbosity which is redirected to log file */
          }  
        }    iagemin= (int) agemin;
      }    iagemax= (int) agemax;
    }    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    /*for(i=1; i <=m ;i++){    j1=0;
      for(k=1; k <=cptcovn; k++){    
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    /*j=cptcoveff;*/
      }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      printf("\n");    
    }    first=1;
    scanf("%d",i);*/    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
          /*for(i1=1; i1<=ncodemax[k1];i1++){
    /* Calculates basic frequencies. Computes observed prevalence at single age        j1++;*/
        and prints on file fileres'p'. */        
         for (i=1; i<=nlstate; i++)  
              for(m=iagemin; m <= iagemax+3; m++)
                prop[i][m]=0.0;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=1; i<=imx; i++) { /* Each individual */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          bool=1;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if  (cptcovn>0) {
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for (z1=1; z1<=cptcoveff; z1++) 
                    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     /* For Powell, parameters are in a vector p[] starting at p[1]                bool=0;
        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) */          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     if(mle==1){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                    if(agev[m][i]==1) agev[m][i]=iagemax+2;
     /*--------- results files --------------*/                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); 
     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= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                    /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
    jk=1;                  prop[s[m][i]][iagemax+3] += weight[i]; 
    fprintf(ficres,"# Parameters\n");                } 
    printf("# Parameters\n");              }
    for(i=1,jk=1; i <=nlstate; i++){            } /* end selection of waves */
      for(k=1; k <=(nlstate+ndeath); k++){          }
        if (k != i)        }
          {        for(i=iagemin; i <= iagemax+3; i++){  
            printf("%d%d ",i,k);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
            fprintf(ficres,"%1d%1d ",i,k);            posprop += prop[jk][i]; 
            for(j=1; j <=ncovmodel; j++){          } 
              printf("%f ",p[jk]);          
              fprintf(ficres,"%f ",p[jk]);          for(jk=1; jk <=nlstate ; jk++){     
              jk++;            if( i <=  iagemax){ 
            }              if(posprop>=1.e-5){ 
            printf("\n");                probs[i][jk][j1]= prop[jk][i]/posprop;
            fprintf(ficres,"\n");              } else{
          }                if(first==1){
      }                  first=0;
    }                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
  if(mle==1){                }
     /* Computing hessian and covariance matrix */              }
     ftolhess=ftol; /* Usually correct */            } 
     hesscov(matcov, p, npar, delti, ftolhess, func);          }/* end jk */ 
  }        }/* end i */ 
     fprintf(ficres,"# Scales\n");      /*} *//* end i1 */
     printf("# Scales\n");    } /* end j1 */
      for(i=1,jk=1; i <=nlstate; i++){    
       for(j=1; j <=nlstate+ndeath; j++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         if (j!=i) {    /*free_vector(pp,1,nlstate);*/
           fprintf(ficres,"%1d%1d",i,j);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           printf("%1d%1d",i,j);  }  /* End of prevalence */
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);  /************* Waves Concatenation ***************/
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
           }  {
           printf("\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           fprintf(ficres,"\n");       Death is a valid wave (if date is known).
         }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      }       and mw[mi+1][i]. dh depends on stepm.
           */
     k=1;  
     fprintf(ficres,"# Covariance\n");    int i, mi, m;
     printf("# Covariance\n");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for(i=1;i<=npar;i++){       double sum=0., jmean=0.;*/
       /*  if (k>nlstate) k=1;    int first;
       i1=(i-1)/(ncovmodel*nlstate)+1;    int j, k=0,jk, ju, jl;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    double sum=0.;
       printf("%s%d%d",alph[k],i1,tab[i]);*/    first=0;
       fprintf(ficres,"%3d",i);    jmin=100000;
       printf("%3d",i);    jmax=-1;
       for(j=1; j<=i;j++){    jmean=0.;
         fprintf(ficres," %.5e",matcov[i][j]);    for(i=1; i<=imx; i++){
         printf(" %.5e",matcov[i][j]);      mi=0;
       }      m=firstpass;
       fprintf(ficres,"\n");      while(s[m][i] <= nlstate){
       printf("\n");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       k++;          mw[++mi][i]=m;
     }        if(m >=lastpass)
              break;
     while((c=getc(ficpar))=='#' && c!= EOF){        else
       ungetc(c,ficpar);          m++;
       fgets(line, MAXLINE, ficpar);      }/* end while */
       puts(line);      if (s[m][i] > nlstate){
       fputs(line,ficparo);        mi++;     /* Death is another wave */
     }        /* if(mi==0)  never been interviewed correctly before death */
     ungetc(c,ficpar);           /* Only death is a correct wave */
          mw[mi][i]=m;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);      }
      
     if (fage <= 2) {      wav[i]=mi;
       bage = agemin;      if(mi==0){
       fage = agemaxpar;        nbwarn++;
     }        if(first==0){
              printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          first=1;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        if(first==1){
            fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);      } /* end mi==0 */
     fgets(line, MAXLINE, ficpar);    } /* End individuals */
     puts(line);  
     fputs(line,ficparo);    for(i=1; i<=imx; i++){
   }      for(mi=1; mi<wav[i];mi++){
   ungetc(c,ficpar);        if (stepm <=0)
            dh[mi][i]=1;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        else{
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            if (agedc[i] < 2*AGESUP) {
                    j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   while((c=getc(ficpar))=='#' && c!= EOF){              if(j==0) j=1;  /* Survives at least one month after exam */
     ungetc(c,ficpar);              else if(j<0){
     fgets(line, MAXLINE, ficpar);                nberr++;
     puts(line);                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]);
     fputs(line,ficparo);                j=1; /* Temporary Dangerous patch */
   }                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   ungetc(c,ficpar);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;              k=k+1;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              if (j >= jmax){
                 jmax=j;
   fscanf(ficpar,"pop_based=%d\n",&popbased);                ijmax=i;
   fprintf(ficparo,"pop_based=%d\n",popbased);                }
   fprintf(ficres,"pop_based=%d\n",popbased);                if (j <= jmin){
                  jmin=j;
   while((c=getc(ficpar))=='#' && c!= EOF){                ijmin=i;
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);              sum=sum+j;
     puts(line);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     fputs(line,ficparo);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   }            }
   ungetc(c,ficpar);          }
           else{
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  /*        if (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]); */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
             k=k+1;
             if (j >= jmax) {
 while((c=getc(ficpar))=='#' && c!= EOF){              jmax=j;
     ungetc(c,ficpar);              ijmax=i;
     fgets(line, MAXLINE, ficpar);            }
     puts(line);            else if (j <= jmin){
     fputs(line,ficparo);              jmin=j;
   }              ijmin=i;
   ungetc(c,ficpar);            }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            /*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]);*/
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            if(j<0){
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);              nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              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]);
             }
 /*------------ gnuplot -------------*/            sum=sum+j;
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);          }
            jk= j/stepm;
 /*------------ free_vector  -------------*/          jl= j -jk*stepm;
  chdir(path);          ju= j -(jk+1)*stepm;
            if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
  free_ivector(wav,1,imx);            if(jl==0){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              dh[mi][i]=jk;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                bh[mi][i]=0;
  free_ivector(num,1,n);            }else{ /* We want a negative bias in order to only have interpolation ie
  free_vector(agedc,1,n);                    * to avoid the price of an extra matrix product in likelihood */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/              dh[mi][i]=jk+1;
  fclose(ficparo);              bh[mi][i]=ju;
  fclose(ficres);            }
           }else{
 /*--------- index.htm --------*/            if(jl <= -ju){
               dh[mi][i]=jk;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
                                     */
   /*--------------- Prevalence limit --------------*/            }
              else{
   strcpy(filerespl,"pl");              dh[mi][i]=jk+1;
   strcat(filerespl,fileres);              bh[mi][i]=ju;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            if(dh[mi][i]==0){
   }              dh[mi][i]=1; /* At least one step */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              bh[mi][i]=ju; /* At least one step */
   fprintf(ficrespl,"#Prevalence limit\n");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   fprintf(ficrespl,"#Age ");            }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          } /* end if mle */
   fprintf(ficrespl,"\n");        }
        } /* end wave */
   prlim=matrix(1,nlstate,1,nlstate);    }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    jmean=sum/k;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    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);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    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);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;  /*********** Tricode ****************************/
   agebase=agemin;  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   agelim=agemaxpar;  {
   ftolpl=1.e-10;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   i1=cptcoveff;    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   if (cptcovn < 1){i1=1;}     * Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   for(cptcov=1;cptcov<=i1;cptcov++){     * nbcode[Tvar[j]][1]= 
     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]);*/    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
         fprintf(ficrespl,"\n#******");    int modmaxcovj=0; /* Modality max of covariates j */
         for(j=1;j<=cptcoveff;j++)    int cptcode=0; /* Modality max of covariates j */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int modmincovj=0; /* Modality min of covariates j */
         fprintf(ficrespl,"******\n");  
          
         for (age=agebase; age<=agelim; age++){    cptcoveff=0; 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   
           fprintf(ficrespl,"%.0f",age );    for (k=-1; k < maxncov; k++) Ndum[k]=0;
           for(i=1; i<=nlstate;i++)    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    /* Loop on covariates without age and products */
         }    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
       }      for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
     }                                 modality of this covariate Vj*/ 
   fclose(ficrespl);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                       * If product of Vn*Vm, still boolean *:
   /*------------- h Pij x at various ages ------------*/                                      * 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   */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                                        modality of the nth covariate of individual i. */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        if (ij > modmaxcovj)
   }          modmaxcovj=ij; 
   printf("Computing pij: result on file '%s' \n", filerespij);        else if (ij < modmincovj) 
            modmincovj=ij; 
   stepsize=(int) (stepm+YEARM-1)/YEARM;        if ((ij < -1) && (ij > NCOVMAX)){
   /*if (stepm<=24) stepsize=2;*/          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
           exit(1);
   agelim=AGESUP;        }else
   hstepm=stepsize*YEARM; /* Every year of age */        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
          /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   k=0;        /* getting the maximum value of the modality of the covariate
   for(cptcov=1;cptcov<=i1;cptcov++){           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           female is 1, then modmaxcovj=1.*/
       k=k+1;      }
         fprintf(ficrespij,"\n#****** ");      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
         for(j=1;j<=cptcoveff;j++)      cptcode=modmaxcovj;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
         fprintf(ficrespij,"******\n");     /*for (i=0; i<=cptcode; i++) {*/
              for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           oldm=oldms;savm=savms;        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);             historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           fprintf(ficrespij,"# Age");      } /* Ndum[-1] number of undefined modalities */
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
               fprintf(ficrespij," %1d-%1d",i,j);      /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
           fprintf(ficrespij,"\n");         If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
           for (h=0; h<=nhstepm; h++){         modmincovj=3; modmaxcovj = 7;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );         There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
             for(i=1; i<=nlstate;i++)         which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
               for(j=1; j<=nlstate+ndeath;j++)         defining two dummy variables: variables V1_1 and V1_2.
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);         nbcode[Tvar[j]][ij]=k;
             fprintf(ficrespij,"\n");         nbcode[Tvar[j]][1]=0;
           }         nbcode[Tvar[j]][2]=1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         nbcode[Tvar[j]][3]=2;
           fprintf(ficrespij,"\n");      */
         }      ij=1; /* ij is similar to i but can jumps over null modalities */
     }      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
   }        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           /*recode from 0 */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             nbcode[Tvar[j]][ij]=k;  /* stores the modality k in an array nbcode. 
   fclose(ficrespij);                                       k is a modality. If we have model=V1+V1*sex 
                                        then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             ij++;
   /*---------- Forecasting ------------------*/          }
   if((stepm == 1) && (strcmp(model,".")==0)){          if (ij > ncodemax[j]) break; 
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        }  /* end of loop on */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      } /* end of loop on modality */ 
     free_matrix(mint,1,maxwav,1,n);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    
     free_vector(weight,1,n);}   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   else{    
     erreur=108;    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     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);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   }     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
       Ndum[ij]++; 
    } 
   /*---------- Health expectancies and variances ------------*/  
    ij=1;
   strcpy(filerest,"t");   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   strcat(filerest,fileres);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   if((ficrest=fopen(filerest,"w"))==NULL) {     if((Ndum[i]!=0) && (i<=ncovcol)){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   }       Tvaraff[ij]=i; /*For printing (unclear) */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       ij++;
      }else
          Tvaraff[ij]=0;
   strcpy(filerese,"e");   }
   strcat(filerese,fileres);   ij--;
   if((ficreseij=fopen(filerese,"w"))==NULL) {   cptcoveff=ij; /*Number of total covariates*/
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }  }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
   
  strcpy(fileresv,"v");  /*********** Health Expectancies ****************/
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }  {
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm;
   k=0;    int nhstepma, nstepma; /* Decreasing with age */
   for(cptcov=1;cptcov<=i1;cptcov++){    double age, agelim, hf;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double ***p3mat;
       k=k+1;    double eip;
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    pstamp(ficreseij);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       fprintf(ficrest,"******\n");    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
       fprintf(ficreseij,"\n#****** ");      for(j=1; j<=nlstate;j++){
       for(j=1;j<=cptcoveff;j++)        fprintf(ficreseij," e%1d%1d ",i,j);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      }
       fprintf(ficreseij,"******\n");      fprintf(ficreseij," e%1d. ",i);
     }
       fprintf(ficresvij,"\n#****** ");    fprintf(ficreseij,"\n");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    
       fprintf(ficresvij,"******\n");    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    }
       oldm=oldms;savm=savms;    else  hstepm=estepm;   
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      /* We compute the life expectancy from trapezoids spaced every estepm months
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     * This is mainly to measure the difference between two models: for example
       oldm=oldms;savm=savms;     * if stepm=24 months pijx are given only every 2 years and by summing them
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     * 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
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");     * to compare the new estimate of Life expectancy with the same linear 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);     * hypothesis. A more precise result, taking into account a more precise
       fprintf(ficrest,"\n");     * curvature will be obtained if estepm is as small as stepm. */
   
       hf=1;    /* For example we decided to compute the life expectancy with the smallest unit */
       if (stepm >= YEARM) hf=stepm/YEARM;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       epj=vector(1,nlstate+1);       nhstepm is the number of hstepm from age to agelim 
       for(age=bage; age <=fage ;age++){       nstepm is the number of stepm from age to agelin. 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       Look at hpijx to understand the reason of that which relies in memory size
         if (popbased==1) {       and note for a fixed period like estepm months */
           for(i=1; i<=nlstate;i++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             prlim[i][i]=probs[(int)age][i][k];       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 
         fprintf(ficrest," %.0f",age);       results. So we changed our mind and took the option of the best precision.
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  
           }    agelim=AGESUP;
           epj[nlstate+1] +=epj[j];    /* If stepm=6 months */
         }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         for(i=1, vepp=0.;i <=nlstate;i++)         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           for(j=1;j <=nlstate;j++)      
             vepp += vareij[i][j][(int)age];  /* nhstepm age range expressed in number of stepm */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         for(j=1;j <=nlstate;j++){    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    /* if (stepm >= YEARM) hstepm=1;*/
         }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         fprintf(ficrest,"\n");    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 */ 
   fclose(ficreseij);      /* if (stepm >= YEARM) hstepm=1;*/
   fclose(ficresvij);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   fclose(ficrest);  
   fclose(ficpar);      /* If stepm=6 months */
   free_vector(epj,1,nlstate+1);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   /*------- Variance limit prevalence------*/        
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   strcpy(fileresvpl,"vpl");      
   strcat(fileresvpl,fileres);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      printf("%d|",(int)age);fflush(stdout);
     exit(0);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   }      
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   k=0;        for(j=1; j<=nlstate;j++)
   for(cptcov=1;cptcov<=i1;cptcov++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       k=k+1;            
       fprintf(ficresvpl,"\n#****** ");            /* 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]);*/
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
       fprintf(ficresvpl,"******\n");  
            fprintf(ficreseij,"%3.0f",age );
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      for(i=1; i<=nlstate;i++){
       oldm=oldms;savm=savms;        eip=0;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        for(j=1; j<=nlstate;j++){
     }          eip +=eij[i][j][(int)age];
  }          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
   fclose(ficresvpl);        fprintf(ficreseij,"%9.4f", eip );
       }
   /*---------- End : free ----------------*/      fprintf(ficreseij,"\n");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      
      }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    printf("\n");
      fprintf(ficlog,"\n");
      
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  }
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  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[] )
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
    {
   free_matrix(matcov,1,npar,1,npar);    /* Covariances of health expectancies eij and of total life expectancies according
   free_vector(delti,1,npar);     to initial status i, ei. .
   free_matrix(agev,1,maxwav,1,imx);    */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
   if(erreur >0)    double age, agelim, hf;
     printf("End of Imach with error %d\n",erreur);    double ***p3matp, ***p3matm, ***varhe;
   else   printf("End of Imach\n");    double **dnewm,**doldm;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    double *xp, *xm;
      double **gp, **gm;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    double ***gradg, ***trgradg;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    int theta;
   /*------ End -----------*/  
     double eip, vip;
   
  end:    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 #ifdef windows    xp=vector(1,npar);
   /* chdir(pathcd);*/    xm=vector(1,npar);
 #endif    dnewm=matrix(1,nlstate*nlstate,1,npar);
  /*system("wgnuplot graph.plt");*/    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  /*system("../gp37mgw/wgnuplot graph.plt");*/    
  /*system("cd ../gp37mgw");*/    pstamp(ficresstdeij);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
  strcpy(plotcmd,GNUPLOTPROGRAM);    fprintf(ficresstdeij,"# Age");
  strcat(plotcmd," ");    for(i=1; i<=nlstate;i++){
  strcat(plotcmd,optionfilegnuplot);      for(j=1; j<=nlstate;j++)
  system(plotcmd);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
 #ifdef windows    }
   while (z[0] != 'q') {    fprintf(ficresstdeij,"\n");
     chdir(path);  
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    pstamp(ficrescveij);
     scanf("%s",z);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     if (z[0] == 'c') system("./imach");    fprintf(ficrescveij,"# Age");
     else if (z[0] == 'e') {    for(i=1; i<=nlstate;i++)
       chdir(path);      for(j=1; j<=nlstate;j++){
       system(optionfilehtm);        cptj= (j-1)*nlstate+i;
     }        for(i2=1; i2<=nlstate;i2++)
     else if (z[0] == 'q') exit(0);          for(j2=1; j2<=nlstate;j2++){
   }            cptj2= (j2-1)*nlstate+i2;
 #endif            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<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+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]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           return 0;
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
           return 0;
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Main Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /* Main ---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%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); */
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n",title, datafile, lastobs, firstpass,lastpass);
     /*
   
   
   
      */
     printf("\nftol=%e \n", ftol);
     printf("stepm=%d \n", stepm);
     printf("ncovcol=%d nlstate=%d \n", ncovcol, nlstate);
     printf("ndeath=%d maxwav=%d mle=%d weight=%d\n", ndeath, maxwav, mle, weightopt);
     printf("model=%s\n",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) { /* Main Wizard */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*  Main data
      */
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
   /* Main decodemodel */
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] is the maximum value of this jth covariate */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              * For k=4 covariates, h goes from 1 to 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
              *     h\k   1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /* codtab[12][3]=1; */
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /* Initialisation of ----------- gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
   
   
     /* Initialisation of --------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
       /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
       /*     gsl_vector_set(x, 0, 0.0268); */
       /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 mortality only */
     /* Standard maximisation */
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* again, to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   
       /* Other stuffs, more or less useful */    
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /* Other results (useful)*/
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
    
       /* ------ Other prevalence ratios------------ */
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
   #ifdef WIN32
      if (_chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n",path);
      if(_getcwd(pathcd,MAXLINE) > 0)
   #else
      if(chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n", path);
      if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.32  
changed lines
  Added in v.1.186


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