Diff for /imach/src/imach.c between versions 1.51 and 1.192

version 1.51, 2002/07/19 12:22:25 version 1.192, 2015/07/16 16:49:02
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.192  2015/07/16 16:49:02  brouard
      Summary: Fixing some outputs
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.191  2015/07/14 10:00:33  brouard
   first survey ("cross") where individuals from different ages are    Summary: Some fixes
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.190  2015/05/05 08:51:13  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: Adding digits in output parameters (7 digits instead of 6)
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Fix 1+age+.
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.189  2015/04/30 14:45:16  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: 0.98q2
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.188  2015/04/30 08:27:53  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    *** empty log message ***
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.187  2015/04/29 09:11:15  brouard
   where the markup *Covariates have to be included here again* invites    *** empty log message ***
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.186  2015/04/23 12:01:52  brouard
     Summary: V1*age is working now, version 0.98q1
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Some codes had been disabled in order to simplify and Vn*age was
   identical for each individual. Also, if a individual missed an    working in the optimization phase, ie, giving correct MLE parameters,
   intermediate interview, the information is lost, but taken into    but, as usual, outputs were not correct and program core dumped.
   account using an interpolation or extrapolation.    
     Revision 1.185  2015/03/11 13:26:42  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: Inclusion of compile and links command line for Intel Compiler
   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 1.184  2015/03/11 11:52:39  brouard
   states. This elementary transition (by month or quarter trimester,    Summary: Back from Windows 8. Intel Compiler
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.183  2015/03/10 20:34:32  brouard
   and the contribution of each individual to the likelihood is simply    Summary: 0.98q0, trying with directest, mnbrak fixed
   hPijx.  
     We use directest instead of original Powell test; probably no
   Also this programme outputs the covariance matrix of the parameters but also    incidence on the results, but better justifications;
   of the life expectancies. It also computes the prevalence limits.    We fixed Numerical Recipes mnbrak routine which was wrong and gave
      wrong results.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.182  2015/02/12 08:19:57  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Trying to keep directest which seems simpler and more general
   from the European Union.    Author: Nicolas Brouard
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.181  2015/02/11 23:22:24  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Summary: Comments on Powell added
   **********************************************************************/  
      Author:
 #include <math.h>  
 #include <stdio.h>    Revision 1.180  2015/02/11 17:33:45  brouard
 #include <stdlib.h>    Summary: Finishing move from main to function (hpijx and prevalence_limit)
 #include <unistd.h>  
     Revision 1.179  2015/01/04 09:57:06  brouard
 #define MAXLINE 256    Summary: back to OS/X
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.178  2015/01/04 09:35:48  brouard
 #define FILENAMELENGTH 80    *** empty log message ***
 /*#define DEBUG*/  
 #define windows    Revision 1.177  2015/01/03 18:40:56  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: Still testing ilc32 on OSX
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.176  2015/01/03 16:45:04  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    *** empty log message ***
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.175  2015/01/03 16:33:42  brouard
 #define NINTERVMAX 8    *** empty log message ***
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.174  2015/01/03 16:15:49  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: Still in cross-compilation
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.173  2015/01/03 12:06:26  brouard
 #define AGESUP 130    Summary: trying to detect cross-compilation
 #define AGEBASE 40  
 #ifdef windows    Revision 1.172  2014/12/27 12:07:47  brouard
 #define DIRSEPARATOR '\\'    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
 #define ODIRSEPARATOR '/'  
 #else    Revision 1.171  2014/12/23 13:26:59  brouard
 #define DIRSEPARATOR '/'    Summary: Back from Visual C
 #define ODIRSEPARATOR '\\'  
 #endif    Still problem with utsname.h on Windows
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Revision 1.170  2014/12/23 11:17:12  brouard
 int erreur; /* Error number */    Summary: Cleaning some \%% back to %%
 int nvar;  
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.169  2014/12/22 23:08:31  brouard
 int ndeath=1; /* Number of dead states */    Summary: 0.98p
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.168  2014/12/22 15:17:42  brouard
 int maxwav; /* Maxim number of waves */    Summary: update
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.167  2014/12/22 13:50:56  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Summary: Testing uname and compiler version and if compiled 32 or 64
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Testing on Linux 64
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.166  2014/12/22 11:40:47  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    *** empty log message ***
 FILE *ficlog;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    Revision 1.165  2014/12/16 11:20:36  brouard
 FILE *ficresprobmorprev;    Summary: After compiling on Visual C
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;    * imach.c (Module): Merging 1.61 to 1.162
 char filerese[FILENAMELENGTH];  
 FILE  *ficresvij;    Revision 1.164  2014/12/16 10:52:11  brouard
 char fileresv[FILENAMELENGTH];    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    * imach.c (Module): Merging 1.61 to 1.162
 char title[MAXLINE];  
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    Revision 1.163  2014/12/16 10:30:11  brouard
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    * imach.c (Module): Merging 1.61 to 1.162
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    Revision 1.162  2014/09/25 11:43:39  brouard
 char filelog[FILENAMELENGTH]; /* Log file */    Summary: temporary backup 0.99!
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Revision 1.1  2014/09/16 11:06:58  brouard
 char popfile[FILENAMELENGTH];    Summary: With some code (wrong) for nlopt
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Author:
   
 #define NR_END 1    Revision 1.161  2014/09/15 20:41:41  brouard
 #define FREE_ARG char*    Summary: Problem with macro SQR on Intel compiler
 #define FTOL 1.0e-10  
     Revision 1.160  2014/09/02 09:24:05  brouard
 #define NRANSI    *** empty log message ***
 #define ITMAX 200  
     Revision 1.159  2014/09/01 10:34:10  brouard
 #define TOL 2.0e-4    Summary: WIN32
     Author: Brouard
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.158  2014/08/27 17:11:51  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    *** empty log message ***
   
 #define GOLD 1.618034    Revision 1.157  2014/08/27 16:26:55  brouard
 #define GLIMIT 100.0    Summary: Preparing windows Visual studio version
 #define TINY 1.0e-20    Author: Brouard
   
 static double maxarg1,maxarg2;    In order to compile on Visual studio, time.h is now correct and time_t
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    and tm struct should be used. difftime should be used but sometimes I
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    just make the differences in raw time format (time(&now).
      Trying to suppress #ifdef LINUX
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Add xdg-open for __linux in order to open default browser.
 #define rint(a) floor(a+0.5)  
     Revision 1.156  2014/08/25 20:10:10  brouard
 static double sqrarg;    *** empty log message ***
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
 int imx;    Author: Brouard
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.154  2014/06/20 17:32:08  brouard
     Summary: Outputs now all graphs of convergence to period prevalence
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
 int m,nb;    Author: Brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.152  2014/06/18 17:54:09  brouard
 double **pmmij, ***probs, ***mobaverage;    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 double dateintmean=0;  
     Revision 1.151  2014/06/18 16:43:30  brouard
 double *weight;    *** empty log message ***
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.150  2014/06/18 16:42:35  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.149  2014/06/18 15:51:14  brouard
     Summary: Some fixes in parameter files errors
 /**************** split *************************/    Author: Nicolas Brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.148  2014/06/17 17:38:48  brouard
    char *s;                             /* pointer */    Summary: Nothing new
    int  l1, l2;                         /* length counters */    Author: Brouard
   
    l1 = strlen( path );                 /* length of path */    Just a new packaging for OS/X version 0.98nS
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    Revision 1.147  2014/06/16 10:33:11  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    *** empty log message ***
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    Revision 1.146  2014/06/16 10:20:28  brouard
 #if     defined(__bsd__)                /* get current working directory */    Summary: Merge
       extern char       *getwd( );    Author: Brouard
   
       if ( getwd( dirc ) == NULL ) {    Merge, before building revised version.
 #else  
       extern char       *getcwd( );    Revision 1.145  2014/06/10 21:23:15  brouard
     Summary: Debugging with valgrind
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Author: Nicolas Brouard
 #endif  
          return( GLOCK_ERROR_GETCWD );    Lot of changes in order to output the results with some covariates
       }    After the Edimburgh REVES conference 2014, it seems mandatory to
       strcpy( name, path );             /* we've got it */    improve the code.
    } else {                             /* strip direcotry from path */    No more memory valgrind error but a lot has to be done in order to
       s++;                              /* after this, the filename */    continue the work of splitting the code into subroutines.
       l2 = strlen( s );                 /* length of filename */    Also, decodemodel has been improved. Tricode is still not
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    optimal. nbcode should be improved. Documentation has been added in
       strcpy( name, s );                /* save file name */    the source code.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.143  2014/01/26 09:45:38  brouard
    }    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.142  2014/01/26 03:57:36  brouard
 #endif    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    s = strrchr( name, '.' );            /* find last / */  
    s++;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.141  2014/01/26 02:42:01  brouard
    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 1.140  2011/09/02 10:37:54  brouard
    return( 0 );                         /* we're done */    Summary: times.h is ok with mingw32 now.
 }  
     Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 /******************************************/    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   
 void replace(char *s, char*t)    Revision 1.138  2010/04/30 18:19:40  brouard
 {    *** empty log message ***
   int i;  
   int lg=20;    Revision 1.137  2010/04/29 18:11:38  brouard
   i=0;    (Module): Checking covariates for more complex models
   lg=strlen(t);    than V1+V2. A lot of change to be done. Unstable.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.136  2010/04/26 20:30:53  brouard
     if (t[i]== '\\') s[i]='/';    (Module): merging some libgsl code. Fixing computation
   }    of likelione (using inter/intrapolation if mle = 0) in order to
 }    get same likelihood as if mle=1.
     Some cleaning of code and comments added.
 int nbocc(char *s, char occ)  
 {    Revision 1.135  2009/10/29 15:33:14  brouard
   int i,j=0;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   int lg=20;  
   i=0;    Revision 1.134  2009/10/29 13:18:53  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 1.133  2009/07/06 10:21:25  brouard
   }    just nforces
   return j;  
 }    Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.131  2009/06/20 16:22:47  brouard
   /* cuts string t into u and v where u is ended by char occ excluding it    Some dimensions resccaled
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  
      gives u="abcedf" and v="ghi2j" */    Revision 1.130  2009/05/26 06:44:34  brouard
   int i,lg,j,p=0;    (Module): Max Covariate is now set to 20 instead of 8. A
   i=0;    lot of cleaning with variables initialized to 0. Trying to make
   for(j=0; j<=strlen(t)-1; j++) {    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    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
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.128  2006/06/30 13:02:05  brouard
     (u[j] = t[j]);    (Module): Clarifications on computing e.j
   }  
      u[p]='\0';    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
    for(j=0; j<= lg; j++) {    imach-114 because nhstepm was no more computed in the age
     if (j>=(p+1))(v[j-p-1] = t[j]);    loop. Now we define nhstepma in the age loop.
   }    (Module): In order to speed up (in case of numerous covariates) we
 }    compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
 /********************** nrerror ********************/    deviation (needs data from the Hessian matrices) which slows the
     computation.
 void nrerror(char error_text[])    In the future we should be able to stop the program is only health
 {    expectancies and graph are needed without standard deviations.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.126  2006/04/28 17:23:28  brouard
   exit(1);    (Module): Yes the sum of survivors was wrong since
 }    imach-114 because nhstepm was no more computed in the age
 /*********************** vector *******************/    loop. Now we define nhstepma in the age loop.
 double *vector(int nl, int nh)    Version 0.98h
 {  
   double *v;    Revision 1.125  2006/04/04 15:20:31  lievre
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Errors in calculation of health expectancies. Age was not initialized.
   if (!v) nrerror("allocation failure in vector");    Forecasting file added.
   return 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).
 /************************ free vector ******************/    The log-likelihood is printed in the log file
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.123  2006/03/20 10:52:43  brouard
   free((FREE_ARG)(v+nl-NR_END));    * imach.c (Module): <title> changed, corresponds to .htm file
 }    name. <head> headers where missing.
   
 /************************ivector *******************************/    * imach.c (Module): Weights can have a decimal point as for
 int *ivector(long nl,long nh)    English (a comma might work with a correct LC_NUMERIC environment,
 {    otherwise the weight is truncated).
   int *v;    Modification of warning when the covariates values are not 0 or
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    1.
   if (!v) nrerror("allocation failure in ivector");    Version 0.98g
   return v-nl+NR_END;  
 }    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 /******************free ivector **************************/    English (a comma might work with a correct LC_NUMERIC environment,
 void free_ivector(int *v, long nl, long nh)    otherwise the weight is truncated).
 {    Modification of warning when the covariates values are not 0 or
   free((FREE_ARG)(v+nl-NR_END));    1.
 }    Version 0.98g
   
 /******************* imatrix *******************************/    Revision 1.121  2006/03/16 17:45:01  lievre
 int **imatrix(long nrl, long nrh, long ncl, long nch)    * imach.c (Module): Comments concerning covariates added
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    * imach.c (Module): refinements in the computation of lli if
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    status=-2 in order to have more reliable computation if stepm is
   int **m;    not 1 month. Version 0.98f
    
   /* allocate pointers to rows */    Revision 1.120  2006/03/16 15:10:38  lievre
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Module): refinements in the computation of lli if
   if (!m) nrerror("allocation failure 1 in matrix()");    status=-2 in order to have more reliable computation if stepm is
   m += NR_END;    not 1 month. Version 0.98f
   m -= nrl;  
      Revision 1.119  2006/03/15 17:42:26  brouard
      (Module): Bug if status = -2, the loglikelihood was
   /* allocate rows and set pointers to them */    computed as likelihood omitting the logarithm. Version O.98e
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.118  2006/03/14 18:20:07  brouard
   m[nrl] += NR_END;    (Module): varevsij Comments added explaining the second
   m[nrl] -= ncl;    table of variances if popbased=1 .
      (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): Function pstamp added
      (Module): Version 0.98d
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.117  2006/03/14 17:16:22  brouard
 }    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 /****************** free_imatrix *************************/    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): Function pstamp added
       int **m;    (Module): Version 0.98d
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.116  2006/03/06 10:29:27  brouard
 {    (Module): Variance-covariance wrong links and
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    varian-covariance of ej. is needed (Saito).
   free((FREE_ARG) (m+nrl-NR_END));  
 }    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.114  2006/02/26 12:57:58  brouard
 {    (Module): Some improvements in processing parameter
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    filename with strsep.
   double **m;  
     Revision 1.113  2006/02/24 14:20:24  brouard
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Module): Memory leaks checks with valgrind and:
   if (!m) nrerror("allocation failure 1 in matrix()");    datafile was not closed, some imatrix were not freed and on matrix
   m += NR_END;    allocation too.
   m -= nrl;  
     Revision 1.112  2006/01/30 09:55:26  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.111  2006/01/25 20:38:18  brouard
   m[nrl] -= ncl;    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    can be a simple dot '.'.
   return m;  
 }    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Revision 1.109  2006/01/24 19:37:15  brouard
 {    (Module): Comments (lines starting with a #) are allowed in data.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.108  2006/01/19 18:05:42  lievre
 }    Gnuplot problem appeared...
     To be fixed
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Revision 1.107  2006/01/19 16:20:37  brouard
 {    Test existence of gnuplot in imach path
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.105  2006/01/05 20:23:19  lievre
   m += NR_END;    *** empty log message ***
   m -= nrl;  
     Revision 1.104  2005/09/30 16:11:43  lievre
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): sump fixed, loop imx fixed, and simplifications.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): If the status is missing at the last wave but we know
   m[nrl] += NR_END;    that the person is alive, then we can code his/her status as -2
   m[nrl] -= ncl;    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Revision 1.103  2005/09/30 15:54:49  lievre
   m[nrl][ncl] += NR_END;    (Module): sump fixed, loop imx fixed, and simplifications.
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.102  2004/09/15 17:31:30  brouard
     m[nrl][j]=m[nrl][j-1]+nlay;    Add the possibility to read data file including tab characters.
    
   for (i=nrl+1; i<=nrh; i++) {    Revision 1.101  2004/09/15 10:38:38  brouard
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Fix on curr_time
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    Revision 1.100  2004/07/12 18:29:06  brouard
   }    Add version for Mac OS X. Just define UNIX in Makefile
   return m;  
 }    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Revision 1.98  2004/05/16 15:05:56  brouard
 {    New version 0.97 . First attempt to estimate force of mortality
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    directly from the data i.e. without the need of knowing the health
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    state at each age, but using a Gompertz model: log u =a + b*age .
   free((FREE_ARG)(m+nrl-NR_END));    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
     cross-longitudinal survey is different from the mortality estimated
 /***************** f1dim *************************/    from other sources like vital statistic data.
 extern int ncom;  
 extern double *pcom,*xicom;    The same imach parameter file can be used but the option for mle should be -3.
 extern double (*nrfunc)(double []);  
      Agnès, who wrote this part of the code, tried to keep most of the
 double f1dim(double x)    former routines in order to include the new code within the former code.
 {  
   int j;    The output is very simple: only an estimate of the intercept and of
   double f;    the slope with 95% confident intervals.
   double *xt;  
      Current limitations:
   xt=vector(1,ncom);    A) Even if you enter covariates, i.e. with the
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   f=(*nrfunc)(xt);    B) There is no computation of Life Expectancy nor Life Table.
   free_vector(xt,1,ncom);  
   return f;    Revision 1.97  2004/02/20 13:25:42  lievre
 }    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Revision 1.96  2003/07/15 15:38:55  brouard
 {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   int iter;    rewritten within the same printf. Workaround: many printfs.
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    Revision 1.95  2003/07/08 07:54:34  brouard
   double ftemp;    * imach.c (Repository):
   double p,q,r,tol1,tol2,u,v,w,x,xm;    (Repository): Using imachwizard code to output a more meaningful covariance
   double e=0.0;    matrix (cov(a12,c31) instead of numbers.
    
   a=(ax < cx ? ax : cx);    Revision 1.94  2003/06/27 13:00:02  brouard
   b=(ax > cx ? ax : cx);    Just cleaning
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    Revision 1.93  2003/06/25 16:33:55  brouard
   for (iter=1;iter<=ITMAX;iter++) {    (Module): On windows (cygwin) function asctime_r doesn't
     xm=0.5*(a+b);    exist so I changed back to asctime which exists.
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    (Module): Version 0.96b
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    Revision 1.92  2003/06/25 16:30:45  brouard
     fprintf(ficlog,".");fflush(ficlog);    (Module): On windows (cygwin) function asctime_r doesn't
 #ifdef DEBUG    exist so I changed back to asctime which exists.
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    Revision 1.91  2003/06/25 15:30:29  brouard
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    * imach.c (Repository): Duplicated warning errors corrected.
 #endif    (Repository): Elapsed time after each iteration is now output. It
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    helps to forecast when convergence will be reached. Elapsed time
       *xmin=x;    is stamped in powell.  We created a new html file for the graphs
       return fx;    concerning matrix of covariance. It has extension -cov.htm.
     }  
     ftemp=fu;    Revision 1.90  2003/06/24 12:34:15  brouard
     if (fabs(e) > tol1) {    (Module): Some bugs corrected for windows. Also, when
       r=(x-w)*(fx-fv);    mle=-1 a template is output in file "or"mypar.txt with the design
       q=(x-v)*(fx-fw);    of the covariance matrix to be input.
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);    Revision 1.89  2003/06/24 12:30:52  brouard
       if (q > 0.0) p = -p;    (Module): Some bugs corrected for windows. Also, when
       q=fabs(q);    mle=-1 a template is output in file "or"mypar.txt with the design
       etemp=e;    of the covariance matrix to be input.
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    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.
       else {  
         d=p/q;    Revision 1.87  2003/06/18 12:26:01  brouard
         u=x+d;    Version 0.96
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    Revision 1.86  2003/06/17 20:04:08  brouard
       }    (Module): Change position of html and gnuplot routines and added
     } else {    routine fileappend.
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }    Revision 1.85  2003/06/17 13:12:43  brouard
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    * imach.c (Repository): Check when date of death was earlier that
     fu=(*f)(u);    current date of interview. It may happen when the death was just
     if (fu <= fx) {    prior to the death. In this case, dh was negative and likelihood
       if (u >= x) a=x; else b=x;    was wrong (infinity). We still send an "Error" but patch by
       SHFT(v,w,x,u)    assuming that the date of death was just one stepm after the
         SHFT(fv,fw,fx,fu)    interview.
         } else {    (Repository): Because some people have very long ID (first column)
           if (u < x) a=u; else b=u;    we changed int to long in num[] and we added a new lvector for
           if (fu <= fw || w == x) {    memory allocation. But we also truncated to 8 characters (left
             v=w;    truncation)
             w=u;    (Repository): No more line truncation errors.
             fv=fw;  
             fw=fu;    Revision 1.84  2003/06/13 21:44:43  brouard
           } else if (fu <= fv || v == x || v == w) {    * imach.c (Repository): Replace "freqsummary" at a correct
             v=u;    place. It differs from routine "prevalence" which may be called
             fv=fu;    many times. Probs is memory consuming and must be used with
           }    parcimony.
         }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   }  
   nrerror("Too many iterations in brent");    Revision 1.83  2003/06/10 13:39:11  lievre
   *xmin=x;    *** empty log message ***
   return fx;  
 }    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 /****************** mnbrak ***********************/  
   */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /*
             double (*func)(double))     Interpolated Markov Chain
 {  
   double ulim,u,r,q, dum;    Short summary of the programme:
   double fu;    
      This program computes Healthy Life Expectancies from
   *fa=(*func)(*ax);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   *fb=(*func)(*bx);    first survey ("cross") where individuals from different ages are
   if (*fb > *fa) {    interviewed on their health status or degree of disability (in the
     SHFT(dum,*ax,*bx,dum)    case of a health survey which is our main interest) -2- at least a
       SHFT(dum,*fb,*fa,dum)    second wave of interviews ("longitudinal") which measure each change
       }    (if any) in individual health status.  Health expectancies are
   *cx=(*bx)+GOLD*(*bx-*ax);    computed from the time spent in each health state according to a
   *fc=(*func)(*cx);    model. More health states you consider, more time is necessary to reach the
   while (*fb > *fc) {    Maximum Likelihood of the parameters involved in the model.  The
     r=(*bx-*ax)*(*fb-*fc);    simplest model is the multinomial logistic model where pij is the
     q=(*bx-*cx)*(*fb-*fa);    probability to be observed in state j at the second wave
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    conditional to be observed in state i at the first wave. Therefore
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     ulim=(*bx)+GLIMIT*(*cx-*bx);    'age' is age and 'sex' is a covariate. If you want to have a more
     if ((*bx-u)*(u-*cx) > 0.0) {    complex model than "constant and age", you should modify the program
       fu=(*func)(u);    where the markup *Covariates have to be included here again* invites
     } else if ((*cx-u)*(u-ulim) > 0.0) {    you to do it.  More covariates you add, slower the
       fu=(*func)(u);    convergence.
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    The advantage of this computer programme, compared to a simple
           SHFT(*fb,*fc,fu,(*func)(u))    multinomial logistic model, is clear when the delay between waves is not
           }    identical for each individual. Also, if a individual missed an
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    intermediate interview, the information is lost, but taken into
       u=ulim;    account using an interpolation or extrapolation.  
       fu=(*func)(u);  
     } else {    hPijx is the probability to be observed in state i at age x+h
       u=(*cx)+GOLD*(*cx-*bx);    conditional to the observed state i at age x. The delay 'h' can be
       fu=(*func)(u);    split into an exact number (nh*stepm) of unobserved intermediate
     }    states. This elementary transition (by month, quarter,
     SHFT(*ax,*bx,*cx,u)    semester or year) is modelled as a multinomial logistic.  The hPx
       SHFT(*fa,*fb,*fc,fu)    matrix is simply the matrix product of nh*stepm elementary matrices
       }    and the contribution of each individual to the likelihood is simply
 }    hPijx.
   
 /*************** linmin ************************/    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
 int ncom;    
 double *pcom,*xicom;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 double (*nrfunc)(double []);             Institut national d'études démographiques, Paris.
      This software have been partly granted by Euro-REVES, a concerted action
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    from the European Union.
 {    It is copyrighted identically to a GNU software product, ie programme and
   double brent(double ax, double bx, double cx,    software can be distributed freely for non commercial use. Latest version
                double (*f)(double), double tol, double *xmin);    can be accessed at http://euroreves.ined.fr/imach .
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
               double *fc, double (*func)(double));    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   int j;    
   double xx,xmin,bx,ax;    **********************************************************************/
   double fx,fb,fa;  /*
      main
   ncom=n;    read parameterfile
   pcom=vector(1,n);    read datafile
   xicom=vector(1,n);    concatwav
   nrfunc=func;    freqsummary
   for (j=1;j<=n;j++) {    if (mle >= 1)
     pcom[j]=p[j];      mlikeli
     xicom[j]=xi[j];    print results files
   }    if mle==1 
   ax=0.0;       computes hessian
   xx=1.0;    read end of parameter file: agemin, agemax, bage, fage, estepm
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);        begin-prev-date,...
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    open gnuplot file
 #ifdef DEBUG    open html file
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 #endif                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   for (j=1;j<=n;j++) {      freexexit2 possible for memory heap.
     xi[j] *= xmin;  
     p[j] += xi[j];    h Pij x                         | pij_nom  ficrestpij
   }     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   free_vector(xicom,1,n);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   free_vector(pcom,1,n);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
 }  
          1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
 /*************** powell ************************/         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
             double (*func)(double []))     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
 {     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));    forecasting if prevfcast==1 prevforecast call prevalence()
   int i,ibig,j;    health expectancies
   double del,t,*pt,*ptt,*xit;    Variance-covariance of DFLE
   double fp,fptt;    prevalence()
   double *xits;     movingaverage()
   pt=vector(1,n);    varevsij() 
   ptt=vector(1,n);    if popbased==1 varevsij(,popbased)
   xit=vector(1,n);    total life expectancies
   xits=vector(1,n);    Variance of period (stable) prevalence
   *fret=(*func)(p);   end
   for (j=1;j<=n;j++) pt[j]=p[j];  */
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  /* #define DEBUG */
     ibig=0;  /* #define DEBUGBRENT */
     del=0.0;  #define POWELL /* Instead of NLOPT */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #define POWELLF1F3 /* Skip test */
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
     for (i=1;i<=n;i++)  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
       printf(" %d %.12f",i, p[i]);  
     fprintf(ficlog," %d %.12f",i, p[i]);  #include <math.h>
     printf("\n");  #include <stdio.h>
     fprintf(ficlog,"\n");  #include <stdlib.h>
     for (i=1;i<=n;i++) {  #include <string.h>
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  #ifdef _WIN32
 #ifdef DEBUG  #include <io.h>
       printf("fret=%lf \n",*fret);  #include <windows.h>
       fprintf(ficlog,"fret=%lf \n",*fret);  #include <tchar.h>
 #endif  #else
       printf("%d",i);fflush(stdout);  #include <unistd.h>
       fprintf(ficlog,"%d",i);fflush(ficlog);  #endif
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  #include <limits.h>
         del=fabs(fptt-(*fret));  #include <sys/types.h>
         ibig=i;  
       }  #if defined(__GNUC__)
 #ifdef DEBUG  #include <sys/utsname.h> /* Doesn't work on Windows */
       printf("%d %.12e",i,(*fret));  #endif
       fprintf(ficlog,"%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  #include <sys/stat.h>
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #include <errno.h>
         printf(" x(%d)=%.12e",j,xit[j]);  /* extern int errno; */
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  
       }  /* #ifdef LINUX */
       for(j=1;j<=n;j++) {  /* #include <time.h> */
         printf(" p=%.12e",p[j]);  /* #include "timeval.h" */
         fprintf(ficlog," p=%.12e",p[j]);  /* #else */
       }  /* #include <sys/time.h> */
       printf("\n");  /* #endif */
       fprintf(ficlog,"\n");  
 #endif  #include <time.h>
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #ifdef GSL
 #ifdef DEBUG  #include <gsl/gsl_errno.h>
       int k[2],l;  #include <gsl/gsl_multimin.h>
       k[0]=1;  #endif
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  
       fprintf(ficlog,"Max: %.12e",(*func)(p));  #ifdef NLOPT
       for (j=1;j<=n;j++) {  #include <nlopt.h>
         printf(" %.12e",p[j]);  typedef struct {
         fprintf(ficlog," %.12e",p[j]);    double (* function)(double [] );
       }  } myfunc_data ;
       printf("\n");  #endif
       fprintf(ficlog,"\n");  
       for(l=0;l<=1;l++) {  /* #include <libintl.h> */
         for (j=1;j<=n;j++) {  /* #define _(String) gettext (String) */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  #define GNUPLOTPROGRAM "gnuplot"
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #define FILENAMELENGTH 132
       }  
 #endif  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
       free_vector(xit,1,n);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
       free_vector(xits,1,n);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  #define NINTERVMAX 8
       return;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     }  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
     for (j=1;j<=n;j++) {  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
       ptt[j]=2.0*p[j]-pt[j];  #define MAXN 20000
       xit[j]=p[j]-pt[j];  #define YEARM 12. /**< Number of months per year */
       pt[j]=p[j];  #define AGESUP 130
     }  #define AGEBASE 40
     fptt=(*func)(ptt);  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
     if (fptt < fp) {  #ifdef _WIN32
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define DIRSEPARATOR '\\'
       if (t < 0.0) {  #define CHARSEPARATOR "\\"
         linmin(p,xit,n,fret,func);  #define ODIRSEPARATOR '/'
         for (j=1;j<=n;j++) {  #else
           xi[j][ibig]=xi[j][n];  #define DIRSEPARATOR '/'
           xi[j][n]=xit[j];  #define CHARSEPARATOR "/"
         }  #define ODIRSEPARATOR '\\'
 #ifdef DEBUG  #endif
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /* $Id$ */
         for(j=1;j<=n;j++){  /* $State$ */
           printf(" %.12e",xit[j]);  
           fprintf(ficlog," %.12e",xit[j]);  char version[]="Imach version 0.98q3, July 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[]="$Revision$ $Date$"; 
         printf("\n");  char strstart[80];
         fprintf(ficlog,"\n");  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 #endif  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       }  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
     }  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   }  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
 }  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
 /**** Prevalence limit ****************/  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   int cptcovprodnoage=0; /**< Number of covariate products without age */   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int cptcoveff=0; /* Total number of covariates to vary for printing results */
 {  int cptcov=0; /* Working variable */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int npar=NPARMAX;
      matrix by transitions matrix until convergence is reached */  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
   int i, ii,j,k;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   double min, max, maxmin, maxmax,sumnew=0.;  int popbased=0;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  int *wav; /* Number of waves for this individuual 0 is possible */
   double **newm;  int maxwav=0; /* Maxim number of waves */
   double agefin, delaymax=50 ; /* Max number of years to converge */  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   for (ii=1;ii<=nlstate+ndeath;ii++)  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     for (j=1;j<=nlstate+ndeath;j++){                     to the likelihood and the sum of weights (done by funcone)*/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int mle=1, weightopt=0;
     }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    cov[1]=1.;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
               * wave mi and wave mi+1 is not an exact multiple of stepm. */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int countcallfunc=0;  /* Count the number of calls to func */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  double jmean=1; /* Mean space between 2 waves */
     newm=savm;  double **matprod2(); /* test */
     /* Covariates have to be included here again */  double **oldm, **newm, **savm; /* Working pointers to matrices */
      cov[2]=agefin;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    /*FILE *fic ; */ /* Used in readdata only */
       for (k=1; k<=cptcovn;k++) {  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  FILE *ficlog, *ficrespow;
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  int globpr=0; /* Global variable for printing or not */
       }  double fretone; /* Only one call to likelihood */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  long ipmx=0; /* Number of contributions */
       for (k=1; k<=cptcovprod;k++)  double sw; /* Sum of weights */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  FILE *ficresilk;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  FILE *ficresprobmorprev;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
     savm=oldm;  char filerese[FILENAMELENGTH];
     oldm=newm;  FILE *ficresstdeij;
     maxmax=0.;  char fileresstde[FILENAMELENGTH];
     for(j=1;j<=nlstate;j++){  FILE *ficrescveij;
       min=1.;  char filerescve[FILENAMELENGTH];
       max=0.;  FILE  *ficresvij;
       for(i=1; i<=nlstate; i++) {  char fileresv[FILENAMELENGTH];
         sumnew=0;  FILE  *ficresvpl;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  char fileresvpl[FILENAMELENGTH];
         prlim[i][j]= newm[i][j]/(1-sumnew);  char title[MAXLINE];
         max=FMAX(max,prlim[i][j]);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
         min=FMIN(min,prlim[i][j]);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       maxmin=max-min;  char command[FILENAMELENGTH];
       maxmax=FMAX(maxmax,maxmin);  int  outcmd=0;
     }  
     if(maxmax < ftolpl){  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       return prlim;  
     }  char filelog[FILENAMELENGTH]; /* Log file */
   }  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 /*************** transition probabilities ***************/  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
   double s1, s2;  /* struct timezone tzp; */
   /*double t34;*/  /* extern int gettimeofday(); */
   int i,j,j1, nc, ii, jj;  struct tm tml, *gmtime(), *localtime();
   
     for(i=1; i<= nlstate; i++){  extern time_t time();
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  struct tm start_time, end_time, curr_time, last_time, forecast_time;
         /*s2 += param[i][j][nc]*cov[nc];*/  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  struct tm tm;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  char strcurr[80], strfor[80];
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char *endptr;
     }  long lval;
     for(j=i+1; j<=nlstate+ndeath;j++){  double dval;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define NR_END 1
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  #define FREE_ARG char*
       }  #define FTOL 1.0e-10
       ps[i][j]=s2;  
     }  #define NRANSI 
   }  #define ITMAX 200 
     /*ps[3][2]=1;*/  
   #define TOL 2.0e-4 
   for(i=1; i<= nlstate; i++){  
      s1=0;  #define CGOLD 0.3819660 
     for(j=1; j<i; j++)  #define ZEPS 1.0e-10 
       s1+=exp(ps[i][j]);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  #define GOLD 1.618034 
     ps[i][i]=1./(s1+1.);  #define GLIMIT 100.0 
     for(j=1; j<i; j++)  #define TINY 1.0e-20 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  static double maxarg1,maxarg2;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   } /* end i */    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #define rint(a) floor(a+0.5)
     for(jj=1; jj<= nlstate+ndeath; jj++){  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
       ps[ii][jj]=0;  #define mytinydouble 1.0e-16
       ps[ii][ii]=1;  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
     }  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   }  /* static double dsqrarg; */
   /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   static double sqrarg;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     for(jj=1; jj<= nlstate+ndeath; jj++){  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
      printf("%lf ",ps[ii][jj]);  int agegomp= AGEGOMP;
    }  
     printf("\n ");  int imx; 
     }  int stepm=1;
     printf("\n ");printf("%lf ",cov[2]);*/  /* Stepm, step in month: minimum step interpolation*/
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  int estepm;
   goto end;*/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     return ps;  
 }  int m,nb;
   long *num;
 /**************** Product of 2 matrices ******************/  int firstpass=0, lastpass=4,*cod, *Tage,*cens;
   int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)                     covariate for which somebody answered excluding 
 {                     undefined. Usually 2: 0 and 1. */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */                               covariate for which somebody answered including 
   /* in, b, out are matrice of pointers which should have been initialized                               undefined. Usually 3: -1, 0 and 1. */
      before: only the contents of out is modified. The function returns  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
      a pointer to pointers identical to out */  double **pmmij, ***probs;
   long i, j, k;  double *ageexmed,*agecens;
   for(i=nrl; i<= nrh; i++)  double dateintmean=0;
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  double *weight;
         out[i][k] +=in[i][j]*b[j][k];  int **s; /* Status */
   double *agedc;
   return out;  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
 }                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
   double  idx; 
 /************* Higher Matrix Product ***************/  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Ndum; /** Freq of modality (tricode */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  int **codtab; /**< codtab=imatrix(1,100,1,10); */
 {  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  double *lsurv, *lpop, *tpop;
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  double ftolhess; /**< Tolerance for computing hessian */
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  /**************** split *************************/
      included manually here.  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
      */    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
   int i, j, d, h, k;    */ 
   double **out, cov[NCOVMAX];    char  *ss;                            /* pointer */
   double **newm;    int   l1=0, l2=0;                             /* length counters */
   
   /* Hstepm could be zero and should return the unit matrix */    l1 = strlen(path );                   /* length of path */
   for (i=1;i<=nlstate+ndeath;i++)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     for (j=1;j<=nlstate+ndeath;j++){    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       oldm[i][j]=(i==j ? 1.0 : 0.0);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       po[i][j][0]=(i==j ? 1.0 : 0.0);      strcpy( name, path );               /* we got the fullname name because no directory */
     }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for(h=1; h <=nhstepm; h++){      /* get current working directory */
     for(d=1; d <=hstepm; d++){      /*    extern  char* getcwd ( char *buf , int len);*/
       newm=savm;  #ifdef WIN32
       /* Covariates have to be included here again */      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
       cov[1]=1.;  #else
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          if (getcwd(dirc, FILENAME_MAX) == NULL) {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #endif
       for (k=1; k<=cptcovage;k++)        return( GLOCK_ERROR_GETCWD );
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      }
       for (k=1; k<=cptcovprod;k++)      /* got dirc from getcwd*/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      l2 = strlen( ss );                  /* length of filename */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      strcpy( name, ss );         /* save file name */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       savm=oldm;      dirc[l1-l2] = '\0';                 /* add zero */
       oldm=newm;      printf(" DIRC2 = %s \n",dirc);
     }    }
     for(i=1; i<=nlstate+ndeath; i++)    /* We add a separator at the end of dirc if not exists */
       for(j=1;j<=nlstate+ndeath;j++) {    l1 = strlen( dirc );                  /* length of directory */
         po[i][j][h]=newm[i][j];    if( dirc[l1-1] != DIRSEPARATOR ){
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      dirc[l1] =  DIRSEPARATOR;
          */      dirc[l1+1] = 0; 
       }      printf(" DIRC3 = %s \n",dirc);
   } /* end h */    }
   return po;    ss = strrchr( name, '.' );            /* find last / */
 }    if (ss >0){
       ss++;
       strcpy(ext,ss);                     /* save extension */
 /*************** log-likelihood *************/      l1= strlen( name);
 double func( double *x)      l2= strlen(ss)+1;
 {      strncpy( finame, name, l1-l2);
   int i, ii, j, k, mi, d, kk;      finame[l1-l2]= 0;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    }
   double **out;  
   double sw; /* Sum of weights */    return( 0 );                          /* we're done */
   double lli; /* Individual log likelihood */  }
   long ipmx;  
   /*extern weight */  
   /* We are differentiating ll according to initial status */  /******************************************/
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  void replace_back_to_slash(char *s, char*t)
     printf(" %d\n",s[4][i]);  {
   */    int i;
   cov[1]=1.;    int lg=0;
     i=0;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    lg=strlen(t);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for(i=0; i<= lg; i++) {
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      (s[i] = t[i]);
     for(mi=1; mi<= wav[i]-1; mi++){      if (t[i]== '\\') s[i]='/';
       for (ii=1;ii<=nlstate+ndeath;ii++)    }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  }
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  char *trimbb(char *out, char *in)
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
         for (kk=1; kk<=cptcovage;kk++) {    char *s;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    s=out;
         }    while (*in != '\0'){
              while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        in++;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      }
         savm=oldm;      *out++ = *in++;
         oldm=newm;    }
            *out='\0';
            return s;
       } /* end mult */  }
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /* char *substrchaine(char *out, char *in, char *chain) */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /* { */
       ipmx +=1;  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
       sw += weight[i];  /*   char *s, *t; */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  /*   t=in;s=out; */
     } /* end of wave */  /*   while ((*in != *chain) && (*in != '\0')){ */
   } /* end of individual */  /*     *out++ = *in++; */
   /*   } */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /*   /\* *in matches *chain *\/ */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /*   while ((*in++ == *chain++) && (*in != '\0')){ */
   return -l;  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
 }  /*   } */
   /*   in--; chain--; */
   /*   while ( (*in != '\0')){ */
 /*********** Maximum Likelihood Estimation ***************/  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*     *out++ = *in++; */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
 {  /*   } */
   int i,j, iter;  /*   *out='\0'; */
   double **xi,*delti;  /*   out=s; */
   double fret;  /*   return out; */
   xi=matrix(1,npar,1,npar);  /* } */
   for (i=1;i<=npar;i++)  char *substrchaine(char *out, char *in, char *chain)
     for (j=1;j<=npar;j++)  {
       xi[i][j]=(i==j ? 1.0 : 0.0);    /* Substract chain 'chain' from 'in', return and output 'out' */
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    /* in="V1+V1*age+age*age+V2", chain="age*age" */
   powell(p,xi,npar,ftol,&iter,&fret,func);  
     char *strloc;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    strcpy (out, in); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
     printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
 }    if(strloc != NULL){ 
       /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
 /**** Computes Hessian and covariance matrix ***/      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      /* strcpy (strloc, strloc +strlen(chain));*/
 {    }
   double  **a,**y,*x,pd;    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
   double **hess;    return out;
   int i, j,jk;  }
   int *indx;  
   
   double hessii(double p[], double delta, int theta, double delti[]);  char *cutl(char *blocc, char *alocc, char *in, char occ)
   double hessij(double p[], double delti[], int i, int j);  {
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
   void ludcmp(double **a, int npar, int *indx, double *d) ;       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef" and alocc="ghi2j".
   hess=matrix(1,npar,1,npar);       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     */
   printf("\nCalculation of the hessian matrix. Wait...\n");    char *s, *t;
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    t=in;s=in;
   for (i=1;i<=npar;i++){    while ((*in != occ) && (*in != '\0')){
     printf("%d",i);fflush(stdout);      *alocc++ = *in++;
     fprintf(ficlog,"%d",i);fflush(ficlog);    }
     hess[i][i]=hessii(p,ftolhess,i,delti);    if( *in == occ){
     /*printf(" %f ",p[i]);*/      *(alocc)='\0';
     /*printf(" %lf ",hess[i][i]);*/      s=++in;
   }    }
     
   for (i=1;i<=npar;i++) {    if (s == t) {/* occ not found */
     for (j=1;j<=npar;j++)  {      *(alocc-(in-s))='\0';
       if (j>i) {      in=s;
         printf(".%d%d",i,j);fflush(stdout);    }
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    while ( *in != '\0'){
         hess[i][j]=hessij(p,delti,i,j);      *blocc++ = *in++;
         hess[j][i]=hess[i][j];        }
         /*printf(" %lf ",hess[i][j]);*/  
       }    *blocc='\0';
     }    return t;
   }  }
   printf("\n");  char *cutv(char *blocc, char *alocc, char *in, char occ)
   fprintf(ficlog,"\n");  {
     /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");       gives blocc="abcdef2ghi" and alocc="j".
         If occ is not found blocc is null and alocc is equal to in. Returns alocc
   a=matrix(1,npar,1,npar);    */
   y=matrix(1,npar,1,npar);    char *s, *t;
   x=vector(1,npar);    t=in;s=in;
   indx=ivector(1,npar);    while (*in != '\0'){
   for (i=1;i<=npar;i++)      while( *in == occ){
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        *blocc++ = *in++;
   ludcmp(a,npar,indx,&pd);        s=in;
       }
   for (j=1;j<=npar;j++) {      *blocc++ = *in++;
     for (i=1;i<=npar;i++) x[i]=0;    }
     x[j]=1;    if (s == t) /* occ not found */
     lubksb(a,npar,indx,x);      *(blocc-(in-s))='\0';
     for (i=1;i<=npar;i++){    else
       matcov[i][j]=x[i];      *(blocc-(in-s)-1)='\0';
     }    in=s;
   }    while ( *in != '\0'){
       *alocc++ = *in++;
   printf("\n#Hessian matrix#\n");    }
   fprintf(ficlog,"\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {    *alocc='\0';
     for (j=1;j<=npar;j++) {    return s;
       printf("%.3e ",hess[i][j]);  }
       fprintf(ficlog,"%.3e ",hess[i][j]);  
     }  int nbocc(char *s, char occ)
     printf("\n");  {
     fprintf(ficlog,"\n");    int i,j=0;
   }    int lg=20;
     i=0;
   /* Recompute Inverse */    lg=strlen(s);
   for (i=1;i<=npar;i++)    for(i=0; i<= lg; i++) {
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    if  (s[i] == occ ) j++;
   ludcmp(a,npar,indx,&pd);    }
     return j;
   /*  printf("\n#Hessian matrix recomputed#\n");  }
   
   for (j=1;j<=npar;j++) {  /* void cutv(char *u,char *v, char*t, char occ) */
     for (i=1;i<=npar;i++) x[i]=0;  /* { */
     x[j]=1;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     lubksb(a,npar,indx,x);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     for (i=1;i<=npar;i++){  /*      gives u="abcdef2ghi" and v="j" *\/ */
       y[i][j]=x[i];  /*   int i,lg,j,p=0; */
       printf("%.3e ",y[i][j]);  /*   i=0; */
       fprintf(ficlog,"%.3e ",y[i][j]);  /*   lg=strlen(t); */
     }  /*   for(j=0; j<=lg-1; j++) { */
     printf("\n");  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     fprintf(ficlog,"\n");  /*   } */
   }  
   */  /*   for(j=0; j<p; j++) { */
   /*     (u[j] = t[j]); */
   free_matrix(a,1,npar,1,npar);  /*   } */
   free_matrix(y,1,npar,1,npar);  /*      u[p]='\0'; */
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);  /*    for(j=0; j<= lg; j++) { */
   free_matrix(hess,1,npar,1,npar);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   /* } */
 }  
   #ifdef _WIN32
 /*************** hessian matrix ****************/  char * strsep(char **pp, const char *delim)
 double hessii( double x[], double delta, int theta, double delti[])  {
 {    char *p, *q;
   int i;           
   int l=1, lmax=20;    if ((p = *pp) == NULL)
   double k1,k2;      return 0;
   double p2[NPARMAX+1];    if ((q = strpbrk (p, delim)) != NULL)
   double res;    {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      *pp = q + 1;
   double fx;      *q = '\0';
   int k=0,kmax=10;    }
   double l1;    else
       *pp = 0;
   fx=func(x);    return p;
   for (i=1;i<=npar;i++) p2[i]=x[i];  }
   for(l=0 ; l <=lmax; l++){  #endif
     l1=pow(10,l);  
     delts=delt;  /********************** nrerror ********************/
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  void nrerror(char error_text[])
       p2[theta]=x[theta] +delt;  {
       k1=func(p2)-fx;    fprintf(stderr,"ERREUR ...\n");
       p2[theta]=x[theta]-delt;    fprintf(stderr,"%s\n",error_text);
       k2=func(p2)-fx;    exit(EXIT_FAILURE);
       /*res= (k1-2.0*fx+k2)/delt/delt; */  }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  /*********************** vector *******************/
        double *vector(int nl, int nh)
 #ifdef DEBUG  {
       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);    double *v;
       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);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 #endif    if (!v) nrerror("allocation failure in vector");
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    return v-nl+NR_END;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  }
         k=kmax;  
       }  /************************ free vector ******************/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  void free_vector(double*v, int nl, int nh)
         k=kmax; l=lmax*10.;  {
       }    free((FREE_ARG)(v+nl-NR_END));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  }
         delts=delt;  
       }  /************************ivector *******************************/
     }  int *ivector(long nl,long nh)
   }  {
   delti[theta]=delts;    int *v;
   return res;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
      if (!v) nrerror("allocation failure in ivector");
 }    return v-nl+NR_END;
   }
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {  /******************free ivector **************************/
   int i;  void free_ivector(int *v, long nl, long nh)
   int l=1, l1, lmax=20;  {
   double k1,k2,k3,k4,res,fx;    free((FREE_ARG)(v+nl-NR_END));
   double p2[NPARMAX+1];  }
   int k;  
   /************************lvector *******************************/
   fx=func(x);  long *lvector(long nl,long nh)
   for (k=1; k<=2; k++) {  {
     for (i=1;i<=npar;i++) p2[i]=x[i];    long *v;
     p2[thetai]=x[thetai]+delti[thetai]/k;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    if (!v) nrerror("allocation failure in ivector");
     k1=func(p2)-fx;    return v-nl+NR_END;
    }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /******************free lvector **************************/
     k2=func(p2)-fx;  void free_lvector(long *v, long nl, long nh)
    {
     p2[thetai]=x[thetai]-delti[thetai]/k;    free((FREE_ARG)(v+nl-NR_END));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  }
     k3=func(p2)-fx;  
    /******************* 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] */ 
     k4=func(p2)-fx;  { 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 #ifdef DEBUG    int **m; 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    /* allocate pointers to rows */ 
 #endif    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   }    if (!m) nrerror("allocation failure 1 in matrix()"); 
   return res;    m += NR_END; 
 }    m -= nrl; 
     
 /************** Inverse of matrix **************/    
 void ludcmp(double **a, int n, int *indx, double *d)    /* allocate rows and set pointers to them */ 
 {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   int i,imax,j,k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double big,dum,sum,temp;    m[nrl] += NR_END; 
   double *vv;    m[nrl] -= ncl; 
      
   vv=vector(1,n);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   *d=1.0;    
   for (i=1;i<=n;i++) {    /* return pointer to array of pointers to rows */ 
     big=0.0;    return m; 
     for (j=1;j<=n;j++)  } 
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  /****************** free_imatrix *************************/
     vv[i]=1.0/big;  void free_imatrix(m,nrl,nrh,ncl,nch)
   }        int **m;
   for (j=1;j<=n;j++) {        long nch,ncl,nrh,nrl; 
     for (i=1;i<j;i++) {       /* free an int matrix allocated by imatrix() */ 
       sum=a[i][j];  { 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       a[i][j]=sum;    free((FREE_ARG) (m+nrl-NR_END)); 
     }  } 
     big=0.0;  
     for (i=j;i<=n;i++) {  /******************* matrix *******************************/
       sum=a[i][j];  double **matrix(long nrl, long nrh, long ncl, long nch)
       for (k=1;k<j;k++)  {
         sum -= a[i][k]*a[k][j];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       a[i][j]=sum;    double **m;
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         imax=i;    if (!m) nrerror("allocation failure 1 in matrix()");
       }    m += NR_END;
     }    m -= nrl;
     if (j != imax) {  
       for (k=1;k<=n;k++) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         dum=a[imax][k];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         a[imax][k]=a[j][k];    m[nrl] += NR_END;
         a[j][k]=dum;    m[nrl] -= ncl;
       }  
       *d = -(*d);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       vv[imax]=vv[j];    return m;
     }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     indx[j]=imax;  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     if (a[j][j] == 0.0) a[j][j]=TINY;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     if (j != n) {     */
       dum=1.0/(a[j][j]);  }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  /*************************free matrix ************************/
   }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   free_vector(vv,1,n);  /* Doesn't work */  {
 ;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 }    free((FREE_ARG)(m+nrl-NR_END));
   }
 void lubksb(double **a, int n, int *indx, double b[])  
 {  /******************* ma3x *******************************/
   int i,ii=0,ip,j;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double sum;  {
      long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (i=1;i<=n;i++) {    double ***m;
     ip=indx[i];  
     sum=b[ip];    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     b[ip]=b[i];    if (!m) nrerror("allocation failure 1 in matrix()");
     if (ii)    m += NR_END;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    m -= nrl;
     else if (sum) ii=i;  
     b[i]=sum;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for (i=n;i>=1;i--) {    m[nrl] += NR_END;
     sum=b[i];    m[nrl] -= ncl;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   }  
 }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 /************ Frequencies ********************/    m[nrl][ncl] += NR_END;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    m[nrl][ncl] -= nll;
 {  /* Some frequencies */    for (j=ncl+1; j<=nch; j++) 
        m[nrl][j]=m[nrl][j-1]+nlay;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    
   int first;    for (i=nrl+1; i<=nrh; i++) {
   double ***freq; /* Frequencies */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   double *pp;      for (j=ncl+1; j<=nch; j++) 
   double pos, k2, dateintsum=0,k2cpt=0;        m[i][j]=m[i][j-1]+nlay;
   FILE *ficresp;    }
   char fileresp[FILENAMELENGTH];    return m; 
      /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   pp=vector(1,nlstate);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    */
   strcpy(fileresp,"p");  }
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /*************************free ma3x ************************/
     printf("Problem with prevalence resultfile: %s\n", fileresp);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);  {
     exit(0);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    free((FREE_ARG)(m+nrl-NR_END));
   j1=0;  }
    
   j=cptcoveff;  /*************** function subdirf ***********/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  char *subdirf(char fileres[])
   {
   first=1;    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   for(k1=1; k1<=j;k1++){    strcat(tmpout,"/"); /* Add to the right */
     for(i1=1; i1<=ncodemax[k1];i1++){    strcat(tmpout,fileres);
       j1++;    return tmpout;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  }
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)    /*************** function subdirf2 ***********/
         for (jk=-1; jk<=nlstate+ndeath; jk++)    char *subdirf2(char fileres[], char *preop)
           for(m=agemin; m <= agemax+3; m++)  {
             freq[i][jk][m]=0;    
          /* Caution optionfilefiname is hidden */
       dateintsum=0;    strcpy(tmpout,optionfilefiname);
       k2cpt=0;    strcat(tmpout,"/");
       for (i=1; i<=imx; i++) {    strcat(tmpout,preop);
         bool=1;    strcat(tmpout,fileres);
         if  (cptcovn>0) {    return tmpout;
           for (z1=1; z1<=cptcoveff; z1++)  }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  /*************** function subdirf3 ***********/
         }  char *subdirf3(char fileres[], char *preop, char *preop2)
         if (bool==1) {  {
           for(m=firstpass; m<=lastpass; m++){    
             k2=anint[m][i]+(mint[m][i]/12.);    /* Caution optionfilefiname is hidden */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    strcpy(tmpout,optionfilefiname);
               if(agev[m][i]==0) agev[m][i]=agemax+1;    strcat(tmpout,"/");
               if(agev[m][i]==1) agev[m][i]=agemax+2;    strcat(tmpout,preop);
               if (m<lastpass) {    strcat(tmpout,preop2);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    strcat(tmpout,fileres);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    return tmpout;
               }  }
                
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  char *asc_diff_time(long time_sec, char ascdiff[])
                 dateintsum=dateintsum+k2;  {
                 k2cpt++;    long sec_left, days, hours, minutes;
               }    days = (time_sec) / (60*60*24);
             }    sec_left = (time_sec) % (60*60*24);
           }    hours = (sec_left) / (60*60) ;
         }    sec_left = (sec_left) %(60*60);
       }    minutes = (sec_left) /60;
            sec_left = (sec_left) % (60);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
       if  (cptcovn>0) {  }
         fprintf(ficresp, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /***************** f1dim *************************/
         fprintf(ficresp, "**********\n#");  extern int ncom; 
       }  extern double *pcom,*xicom;
       for(i=1; i<=nlstate;i++)  extern double (*nrfunc)(double []); 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);   
       fprintf(ficresp, "\n");  double f1dim(double x) 
        { 
       for(i=(int)agemin; i <= (int)agemax+3; i++){    int j; 
         if(i==(int)agemax+3){    double f;
           fprintf(ficlog,"Total");    double *xt; 
         }else{   
           if(first==1){    xt=vector(1,ncom); 
             first=0;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
             printf("See log file for details...\n");    f=(*nrfunc)(xt); 
           }    free_vector(xt,1,ncom); 
           fprintf(ficlog,"Age %d", i);    return f; 
         }  } 
         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++){    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
           for(m=-1, pos=0; m <=0 ; m++)     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
             pos += freq[jk][m][i];     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
           if(pp[jk]>=1.e-10){     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
             if(first==1){     * returned function value. 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    */
             }    int iter; 
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    double a,b,d,etemp;
           }else{    double fu=0,fv,fw,fx;
             if(first==1)    double ftemp=0.;
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double e=0.0; 
           }   
         }    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
             if(first==1)      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      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);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
           }else{  #endif
             if(first==1)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        *xmin=x; 
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        return fx; 
           }      } 
           if( i <= (int) agemax){      ftemp=fu;
             if(pos>=1.e-5){      if (fabs(e) > tol1) { 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        r=(x-w)*(fx-fv); 
               probs[i][jk][j1]= pp[jk]/pos;        q=(x-v)*(fx-fw); 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        p=(x-v)*q-(x-w)*r; 
             }        q=2.0*(q-r); 
             else        if (q > 0.0) p = -p; 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        q=fabs(q); 
           }        etemp=e; 
         }        e=d; 
                if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         for(jk=-1; jk <=nlstate+ndeath; jk++)          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           for(m=-1; m <=nlstate+ndeath; m++)        else { 
             if(freq[jk][m][i] !=0 ) {          d=p/q; 
             if(first==1)          u=x+d; 
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          if (u-a < tol2 || b-u < tol2) 
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);            d=SIGN(tol1,xm-x); 
             }        } 
         if(i <= (int) agemax)      } else { 
           fprintf(ficresp,"\n");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         if(first==1)      } 
           printf("Others in log...\n");      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         fprintf(ficlog,"\n");      fu=(*f)(u); 
       }      if (fu <= fx) { 
     }        if (u >= x) a=x; else b=x; 
   }        SHFT(v,w,x,u) 
   dateintmean=dateintsum/k2cpt;        SHFT(fv,fw,fx,fu) 
        } else { 
   fclose(ficresp);        if (u < x) a=u; else b=u; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        if (fu <= fw || w == x) { 
   free_vector(pp,1,nlstate);          v=w; 
            w=u; 
   /* End of Freq */          fv=fw; 
 }          fw=fu; 
         } else if (fu <= fv || v == x || v == w) { 
 /************ Prevalence ********************/          v=u; 
 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)          fv=fu; 
 {  /* Some frequencies */        } 
        } 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    } 
   double ***freq; /* Frequencies */    nrerror("Too many iterations in brent"); 
   double *pp;    *xmin=x; 
   double pos, k2;    return fx; 
   } 
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /****************** mnbrak ***********************/
    
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   j1=0;              double (*func)(double)) 
    { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
   j=cptcoveff;  the downhill direction (defined by the function as evaluated at the initial points) and returns
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
    values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
   for(k1=1; k1<=j;k1++){     */
     for(i1=1; i1<=ncodemax[k1];i1++){    double ulim,u,r,q, dum;
       j1++;    double fu; 
        
       for (i=-1; i<=nlstate+ndeath; i++)      double scale=10.;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      int iterscale=0;
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
          *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
       for (i=1; i<=imx; i++) {  
         bool=1;  
         if  (cptcovn>0) {    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
           for (z1=1; z1<=cptcoveff; z1++)    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    /*   *bx = *ax - (*ax - *bx)/scale; */
               bool=0;    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
         }    /* } */
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){    if (*fb > *fa) { 
             k2=anint[m][i]+(mint[m][i]/12.);      SHFT(dum,*ax,*bx,dum) 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      SHFT(dum,*fb,*fa,dum) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    *cx=(*bx)+GOLD*(*bx-*ax); 
               if (m<lastpass) {    *fc=(*func)(*cx); 
                 if (calagedate>0)  #ifdef DEBUG
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
                 else    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  #endif
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
               }      r=(*bx-*ax)*(*fb-*fc); 
             }      q=(*bx-*cx)*(*fb-*fa); 
           }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
       }      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
       for(i=(int)agemin; i <= (int)agemax+3; i++){      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
         for(jk=1; jk <=nlstate ; jk++){        fu=(*func)(u); 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  #ifdef DEBUG
             pp[jk] += freq[jk][m][i];        /* f(x)=A(x-u)**2+f(u) */
         }        double A, fparabu; 
         for(jk=1; jk <=nlstate ; jk++){        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
           for(m=-1, pos=0; m <=0 ; m++)        fparabu= *fa - A*(*ax-u)*(*ax-u);
             pos += freq[jk][m][i];        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);
                /* And thus,it can be that fu > *fc even if fparabu < *fc */
         for(jk=1; jk <=nlstate ; jk++){        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
             pp[jk] += freq[jk][m][i];        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
         }  #endif 
          #ifdef MNBRAKORIGINAL
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  #else
          /*       if (fu > *fc) { */
         for(jk=1; jk <=nlstate ; jk++){      /* #ifdef DEBUG */
           if( i <= (int) agemax){  /*       printf("mnbrak4  fu > fc \n"); */
             if(pos>=1.e-5){  /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
               probs[i][jk][j1]= pp[jk]/pos;  /* #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 *\\/ *\/ */
         }/* end jk */  /*      dum=u; /\* Shifting c and u *\/ */
       }/* end i */  /*      u = *cx; */
     } /* end i1 */  /*      *cx = dum; */
   } /* end k1 */  /*      dum = fu; */
   /*      fu = *fc; */
    /*      *fc =dum; */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*       } else { /\* end *\/ */
   free_vector(pp,1,nlstate);  /* #ifdef DEBUG */
    /*       printf("mnbrak3  fu < fc \n"); */
 }  /* End of Freq */  /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
   /* #endif */
 /************* Waves Concatenation ***************/  /*      dum=u; /\* Shifting c and u *\/ */
   /*      u = *cx; */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  /*      *cx = dum; */
 {  /*      dum = fu; */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  /*      fu = *fc; */
      Death is a valid wave (if date is known).  /*      *fc =dum; */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  /*       } */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  #ifdef DEBUG
      and mw[mi+1][i]. dh depends on stepm.        printf("mnbrak34  fu < or >= fc \n");
      */        fprintf(ficlog, "mnbrak34 fu < fc\n");
   #endif
   int i, mi, m;        dum=u; /* Shifting c and u */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        u = *cx;
      double sum=0., jmean=0.;*/        *cx = dum;
   int first;        dum = fu;
   int j, k=0,jk, ju, jl;        fu = *fc;
   double sum=0.;        *fc =dum;
   first=0;  #endif
   jmin=1e+5;      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   jmax=-1;  #ifdef DEBUG
   jmean=0.;        printf("mnbrak2  u after c but before ulim\n");
   for(i=1; i<=imx; i++){        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
     mi=0;  #endif
     m=firstpass;        fu=(*func)(u); 
     while(s[m][i] <= nlstate){        if (fu < *fc) { 
       if(s[m][i]>=1)  #ifdef DEBUG
         mw[++mi][i]=m;        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
       if(m >=lastpass)        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
         break;  #endif
       else          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         m++;          SHFT(*fb,*fc,fu,(*func)(u)) 
     }/* end while */        } 
     if (s[m][i] > nlstate){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
       mi++;     /* Death is another wave */  #ifdef DEBUG
       /* if(mi==0)  never been interviewed correctly before death */        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
          /* Only death is a correct wave */        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
       mw[mi][i]=m;  #endif
     }        u=ulim; 
         fu=(*func)(u); 
     wav[i]=mi;      } else { /* u could be left to b (if r > q parabola has a maximum) */
     if(mi==0){  #ifdef DEBUG
       if(first==0){        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
         first=1;  #endif
       }        u=(*cx)+GOLD*(*cx-*bx); 
       if(first==1){        fu=(*func)(u); 
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);      } /* end tests */
       }      SHFT(*ax,*bx,*cx,u) 
     } /* end mi==0 */      SHFT(*fa,*fb,*fc,fu) 
   }  #ifdef DEBUG
         printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
   for(i=1; i<=imx; i++){        fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
     for(mi=1; mi<wav[i];mi++){  #endif
       if (stepm <=0)    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
         dh[mi][i]=1;  } 
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {  /*************** linmin ************************/
           if (agedc[i] < 2*AGESUP) {  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
           if(j==0) j=1;  /* Survives at least one month after exam */  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
           k=k+1;  the value of func at the returned location p . This is actually all accomplished by calling the
           if (j >= jmax) jmax=j;  routines mnbrak and brent .*/
           if (j <= jmin) jmin=j;  int ncom; 
           sum=sum+j;  double *pcom,*xicom;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  double (*nrfunc)(double []); 
           }   
         }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         else{  { 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    double brent(double ax, double bx, double cx, 
           k=k+1;                 double (*f)(double), double tol, double *xmin); 
           if (j >= jmax) jmax=j;    double f1dim(double x); 
           else if (j <= jmin)jmin=j;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */                double *fc, double (*func)(double)); 
           sum=sum+j;    int j; 
         }    double xx,xmin,bx,ax; 
         jk= j/stepm;    double fx,fb,fa;
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;    double scale=10., axs, xxs, xxss; /* Scale added for infinity */
         if(jl <= -ju)   
           dh[mi][i]=jk;    ncom=n; 
         else    pcom=vector(1,n); 
           dh[mi][i]=jk+1;    xicom=vector(1,n); 
         if(dh[mi][i]==0)    nrfunc=func; 
           dh[mi][i]=1; /* At least one step */    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);    /* axs=0.0; */
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    /* xxss=1; /\* 1 and using scale *\/ */
  }    xxs=1;
     /* do{ */
 /*********** Tricode ****************************/      ax=0.;
 void tricode(int *Tvar, int **nbcode, int imx)      xx= xxs;
 {      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
   int Ndum[20],ij=1, k, j, i;      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
   int cptcode=0;      /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
   cptcoveff=0;      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
        /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
   for (k=0; k<19; k++) Ndum[k]=0;      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
   for (k=1; k<=7; k++) ncodemax[k]=0;      /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
     /*   if (fx != fx){ */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    /*    xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
     for (i=1; i<=imx; i++) {    /*    printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx); */
       ij=(int)(covar[Tvar[j]][i]);    /*   } */
       Ndum[ij]++;    /* }while(fx != fx); */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;  #ifdef DEBUGLINMIN
     }    printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
   #endif
     for (i=0; i<=cptcode; i++) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
       if(Ndum[i]!=0) ncodemax[j]++;    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
     }    /* fmin = f(p[j] + xmin * xi[j]) */
     ij=1;    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
     /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
   #ifdef DEBUG
     for (i=1; i<=ncodemax[j]; i++) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (k=0; k<=19; k++) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         if (Ndum[k] != 0) {  #endif
           nbcode[Tvar[j]][ij]=k;  #ifdef DEBUGLINMIN
              printf("linmin end ");
           ij++;  #endif
         }    for (j=1;j<=n;j++) { 
         if (ij > ncodemax[j]) break;      /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
       }        xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
     }      /* if(xxs <1.0) */
   }        /*   printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */
       p[j] += xi[j]; /* Parameters values are updated accordingly */
  for (k=0; k<19; k++) Ndum[k]=0;    } 
     /* printf("\n"); */
  for (i=1; i<=ncovmodel-2; i++) {  #ifdef DEBUGLINMIN
    ij=Tvar[i];    printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
    Ndum[ij]++;    for (j=1;j<=n;j++) { 
  }      printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
       if(j % ncovmodel == 0)
  ij=1;        printf("\n");
  for (i=1; i<=10; i++) {    }
    if((Ndum[i]!=0) && (i<=ncovcol)){  #endif
      Tvaraff[ij]=i;    free_vector(xicom,1,n); 
      ij++;    free_vector(pcom,1,n); 
    }  } 
  }  
    
  cptcoveff=ij-1;  /*************** powell ************************/
 }  /*
   Minimization of a function func of n variables. Input consists of an initial starting point
 /*********** Health Expectancies ****************/  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )  such that failure to decrease by more than this amount on one iteration signals doneness. On
   output, p is set to the best point found, xi is the then-current direction set, fret is the returned
 {  function value at p , and iter is the number of iterations taken. The routine linmin is used.
   /* Health expectancies */   */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   double age, agelim, hf;              double (*func)(double [])) 
   double ***p3mat,***varhe;  { 
   double **dnewm,**doldm;    void linmin(double p[], double xi[], int n, double *fret, 
   double *xp;                double (*func)(double [])); 
   double **gp, **gm;    int i,ibig,j; 
   double ***gradg, ***trgradg;    double del,t,*pt,*ptt,*xit;
   int theta;    double directest;
     double fp,fptt;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    double *xits;
   xp=vector(1,npar);    int niterf, itmp;
   dnewm=matrix(1,nlstate*2,1,npar);  
   doldm=matrix(1,nlstate*2,1,nlstate*2);    pt=vector(1,n); 
      ptt=vector(1,n); 
   fprintf(ficreseij,"# Health expectancies\n");    xit=vector(1,n); 
   fprintf(ficreseij,"# Age");    xits=vector(1,n); 
   for(i=1; i<=nlstate;i++)    *fret=(*func)(p); 
     for(j=1; j<=nlstate;j++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
       fprintf(ficreseij," %1d-%1d (SE)",i,j);      rcurr_time = time(NULL);  
   fprintf(ficreseij,"\n");    for (*iter=1;;++(*iter)) { 
       fp=(*fret); /* From former iteration or initial value */
   if(estepm < stepm){      ibig=0; 
     printf ("Problem %d lower than %d\n",estepm, stepm);      del=0.0; 
   }      rlast_time=rcurr_time;
   else  hstepm=estepm;        /* (void) gettimeofday(&curr_time,&tzp); */
   /* We compute the life expectancy from trapezoids spaced every estepm months      rcurr_time = time(NULL);  
    * This is mainly to measure the difference between two models: for example      curr_time = *localtime(&rcurr_time);
    * if stepm=24 months pijx are given only every 2 years and by summing them      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
    * we are calculating an estimate of the Life Expectancy assuming a linear      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
    * progression inbetween and thus overestimating or underestimating according  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
    * to the curvature of the survival function. If, for the same date, we      for (i=1;i<=n;i++) {
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        printf(" %d %.12f",i, p[i]);
    * to compare the new estimate of Life expectancy with the same linear        fprintf(ficlog," %d %.12lf",i, p[i]);
    * hypothesis. A more precise result, taking into account a more precise        fprintf(ficrespow," %.12lf", p[i]);
    * curvature will be obtained if estepm is as small as stepm. */      }
       printf("\n");
   /* For example we decided to compute the life expectancy with the smallest unit */      fprintf(ficlog,"\n");
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      fprintf(ficrespow,"\n");fflush(ficrespow);
      nhstepm is the number of hstepm from age to agelim      if(*iter <=3){
      nstepm is the number of stepm from age to agelin.        tml = *localtime(&rcurr_time);
      Look at hpijx to understand the reason of that which relies in memory size        strcpy(strcurr,asctime(&tml));
      and note for a fixed period like estepm months */        rforecast_time=rcurr_time; 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        itmp = strlen(strcurr);
      survival function given by stepm (the optimization length). Unfortunately it        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
      means that if the survival funtion is printed only each two years of age and if          strcurr[itmp-1]='\0';
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
      results. So we changed our mind and took the option of the best precision.        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   */        for(niterf=10;niterf<=30;niterf+=10){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
           forecast_time = *localtime(&rforecast_time);
   agelim=AGESUP;          strcpy(strfor,asctime(&forecast_time));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          itmp = strlen(strfor);
     /* nhstepm age range expressed in number of stepm */          if(strfor[itmp-1]=='\n')
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          strfor[itmp-1]='\0';
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          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);
     /* if (stepm >= YEARM) hstepm=1;*/          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);
     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*2);      for (i=1;i<=n;i++) { /* For each direction i */
     gp=matrix(0,nhstepm,1,nlstate*2);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
     gm=matrix(0,nhstepm,1,nlstate*2);        fptt=(*fret); 
   #ifdef DEBUG
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    #endif
              printf("%d",i);fflush(stdout); /* print direction (parameter) i */
         fprintf(ficlog,"%d",i);fflush(ficlog);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                                       /* Outputs are fret(new point p) p is updated and xit rescaled */
     /* Computing Variances of health expectancies */        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
           /* because that direction will be replaced unless the gain del is small */
      for(theta=1; theta <=npar; theta++){          /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
       for(i=1; i<=npar; i++){          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          /* with the new direction. */
       }          del=fabs(fptt-(*fret)); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ibig=i; 
          } 
       cptj=0;  #ifdef DEBUG
       for(j=1; j<= nlstate; j++){        printf("%d %.12e",i,(*fret));
         for(i=1; i<=nlstate; i++){        fprintf(ficlog,"%d %.12e",i,(*fret));
           cptj=cptj+1;        for (j=1;j<=n;j++) {
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          printf(" x(%d)=%.12e",j,xit[j]);
           }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }        }
       }        for(j=1;j<=n;j++) {
                printf(" p(%d)=%.12e",j,p[j]);
                fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       for(i=1; i<=npar; i++)        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        printf("\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          fprintf(ficlog,"\n");
        #endif
       cptj=0;      } /* end loop on each direction i */
       for(j=1; j<= nlstate; j++){      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
         for(i=1;i<=nlstate;i++){      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
           cptj=cptj+1;      /* New value of last point Pn is not computed, P(n-1) */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
           }        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
         }        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
       }        /* decreased of more than 3.84  */
       for(j=1; j<= nlstate*2; j++)        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
         for(h=0; h<=nhstepm-1; h++){        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        /* By adding 10 parameters more the gain should be 18.31 */
         }  
      }        /* Starting the program with initial values given by a former maximization will simply change */
            /* the scales of the directions and the directions, because the are reset to canonical directions */
 /* End theta */        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
         /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  #ifdef DEBUG
         int k[2],l;
      for(h=0; h<=nhstepm-1; h++)        k[0]=1;
       for(j=1; j<=nlstate*2;j++)        k[1]=-1;
         for(theta=1; theta <=npar; theta++)        printf("Max: %.12e",(*func)(p));
           trgradg[h][j][theta]=gradg[h][theta][j];        fprintf(ficlog,"Max: %.12e",(*func)(p));
              for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
      for(i=1;i<=nlstate*2;i++)          fprintf(ficlog," %.12e",p[j]);
       for(j=1;j<=nlstate*2;j++)        }
         varhe[i][j][(int)age] =0.;        printf("\n");
         fprintf(ficlog,"\n");
      printf("%d|",(int)age);fflush(stdout);        for(l=0;l<=1;l++) {
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);          for (j=1;j<=n;j++) {
      for(h=0;h<=nhstepm-1;h++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       for(k=0;k<=nhstepm-1;k++){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          }
         for(i=1;i<=nlstate*2;i++)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           for(j=1;j<=nlstate*2;j++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        }
       }  #endif
     }  
     /* Computing expectancies */  
     for(i=1; i<=nlstate;i++)        free_vector(xit,1,n); 
       for(j=1; j<=nlstate;j++)        free_vector(xits,1,n); 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        free_vector(ptt,1,n); 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        free_vector(pt,1,n); 
                  return; 
 /* 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]);*/      } /* enough precision */ 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         }      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
         ptt[j]=2.0*p[j]-pt[j]; 
     fprintf(ficreseij,"%3.0f",age );        xit[j]=p[j]-pt[j]; 
     cptj=0;        pt[j]=p[j]; 
     for(i=1; i<=nlstate;i++)      } 
       for(j=1; j<=nlstate;j++){      fptt=(*func)(ptt); /* f_3 */
         cptj++;  #ifdef POWELLF1F3
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );  #else
       }      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
     fprintf(ficreseij,"\n");  #endif
            /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
     free_matrix(gm,0,nhstepm,1,nlstate*2);        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
     free_matrix(gp,0,nhstepm,1,nlstate*2);        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* 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); */
   printf("\n");  #ifdef NRCORIGINAL
   fprintf(ficlog,"\n");        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   #else
   free_vector(xp,1,npar);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
   free_matrix(dnewm,1,nlstate*2,1,npar);        t= t- del*SQR(fp-fptt);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  #endif
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
 }  #ifdef DEBUG
         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);
 /************ Variance ******************/        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);
 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)        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
 {               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   /* Variance of health expectancies */        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   /* double **newm;*/        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);
   double **dnewm,**doldm;        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);
   double **dnewmp,**doldmp;  #endif
   int i, j, nhstepm, hstepm, h, nstepm ;  #ifdef POWELLORIGINAL
   int k, cptcode;        if (t < 0.0) { /* Then we use it for new direction */
   double *xp;  #else
   double **gp, **gm;  /* for var eij */        if (directest*t < 0.0) { /* Contradiction between both tests */
   double ***gradg, ***trgradg; /*for var eij */          printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
   double **gradgp, **trgradgp; /* for var p point j */          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   double *gpp, *gmp; /* for var p point j */          fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   double ***p3mat;        } 
   double age,agelim, hf;        if (directest < 0.0) { /* Then we use it for new direction */
   int theta;  #endif
   char digit[4];  #ifdef DEBUGLINMIN
   char digitp[16];          printf("Before linmin in direction P%d-P0\n",n);
           for (j=1;j<=n;j++) { 
   char fileresprobmorprev[FILENAMELENGTH];            printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             if(j % ncovmodel == 0)
   if(popbased==1)              printf("\n");
     strcpy(digitp,"-populbased-");          }
   else  #endif
     strcpy(digitp,"-stablbased-");          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
   #ifdef DEBUGLINMIN
   strcpy(fileresprobmorprev,"prmorprev");          for (j=1;j<=n;j++) { 
   sprintf(digit,"%-d",ij);            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/            if(j % ncovmodel == 0)
   strcat(fileresprobmorprev,digit); /* Tvar to be done */              printf("\n");
   strcat(fileresprobmorprev,digitp); /* Popbased or not */          }
   strcat(fileresprobmorprev,fileres);  #endif
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {          for (j=1;j<=n;j++) { 
     printf("Problem with resultfile: %s\n", fileresprobmorprev);            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
   }          }
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");  
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);  #ifdef DEBUG
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     fprintf(ficresprobmorprev," p.%-d SE",j);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(i=1; i<=nlstate;i++)          for(j=1;j<=n;j++){
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);            printf(" %.12e",xit[j]);
   }              fprintf(ficlog," %.12e",xit[j]);
   fprintf(ficresprobmorprev,"\n");          }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          printf("\n");
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          fprintf(ficlog,"\n");
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);  #endif
     exit(0);        } /* end of t or directest negative */
   }  #ifdef POWELLF1F3
   else{  #else
     fprintf(ficgp,"\n# Routine varevsij");      } /* end if (fptt < fp)  */
   }  #endif
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    } /* loop iteration */ 
     printf("Problem with html file: %s\n", optionfilehtm);  } 
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);  
     exit(0);  /**** Prevalence limit (stable or period prevalence)  ****************/
   }  
   else{  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");  {
   }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);       matrix by transitions matrix until convergence is reached */
     
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");    int i, ii,j,k;
   fprintf(ficresvij,"# Age");    double min, max, maxmin, maxmax,sumnew=0.;
   for(i=1; i<=nlstate;i++)    /* double **matprod2(); */ /* test */
     for(j=1; j<=nlstate;j++)    double **out, cov[NCOVMAX+1], **pmij();
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    double **newm;
   fprintf(ficresvij,"\n");    double agefin, delaymax=50 ; /* Max number of years to converge */
     
   xp=vector(1,npar);    for (ii=1;ii<=nlstate+ndeath;ii++)
   dnewm=matrix(1,nlstate,1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   doldm=matrix(1,nlstate,1,nlstate);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);      }
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    
     cov[1]=1.;
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    
   gpp=vector(nlstate+1,nlstate+ndeath);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   gmp=vector(nlstate+1,nlstate+ndeath);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/      newm=savm;
        /* Covariates have to be included here again */
   if(estepm < stepm){      cov[2]=agefin;
     printf ("Problem %d lower than %d\n",estepm, stepm);      if(nagesqr==1)
   }        cov[3]= agefin*agefin;;
   else  hstepm=estepm;        for (k=1; k<=cptcovn;k++) {
   /* For example we decided to compute the life expectancy with the smallest unit */        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        /*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]]);*/
      nhstepm is the number of hstepm from age to agelim      }
      nstepm is the number of stepm from age to agelin.      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
      Look at hpijx to understand the reason of that which relies in memory size      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
      and note for a fixed period like k years */      for (k=1; k<=cptcovprod;k++) /* Useless */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      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      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      results. So we changed our mind and took the option of the best precision.      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   */      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   agelim = AGESUP;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      savm=oldm;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      oldm=newm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      maxmax=0.;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for(j=1;j<=nlstate;j++){
     gp=matrix(0,nhstepm,1,nlstate);        min=1.;
     gm=matrix(0,nhstepm,1,nlstate);        max=0.;
         for(i=1; i<=nlstate; i++) {
           sumnew=0;
     for(theta=1; theta <=npar; theta++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       for(i=1; i<=npar; i++){ /* Computes gradient */          prlim[i][j]= newm[i][j]/(1-sumnew);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
       }          max=FMAX(max,prlim[i][j]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            min=FMIN(min,prlim[i][j]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
         maxmin=max-min;
       if (popbased==1) {        maxmax=FMAX(maxmax,maxmin);
         for(i=1; i<=nlstate;i++)      } /* j loop */
           prlim[i][i]=probs[(int)age][i][ij];      if(maxmax < ftolpl){
       }        return prlim;
        }
       for(j=1; j<= nlstate; j++){    } /* age loop */
         for(h=0; h<=nhstepm; h++){    return prlim; /* should not reach here */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  /*************** transition probabilities ***************/ 
       }  
       /* This for computing forces of mortality (h=1)as a weighted average */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){  {
         for(i=1; i<= nlstate; i++)    /* According to parameters values stored in x and the covariate's values stored in cov,
           gpp[j] += prlim[i][i]*p3mat[i][j][1];       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).
       /* end force of mortality */       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(i=1; i<=npar; i++) /* Computes gradient */       ncth covariate in the global vector x is given by the formula:
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
         sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       if (popbased==1) {       Outputs ps[i][j] the probability to be observed in j being in j according to
         for(i=1; i<=nlstate;i++)       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
           prlim[i][i]=probs[(int)age][i][ij];    */
       }    double s1, lnpijopii;
     /*double t34;*/
       for(j=1; j<= nlstate; j++){    int i,j, nc, ii, jj;
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for(i=1; i<= nlstate; i++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        for(j=1; j<i;j++){
         }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       }            /*lnpijopii += param[i][j][nc]*cov[nc];*/
       /* This for computing force of mortality (h=1)as a weighted average */            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         for(i=1; i<= nlstate; i++)          }
           gmp[j] += prlim[i][i]*p3mat[i][j][1];          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       }      /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       /* end force of mortality */        }
         for(j=i+1; j<=nlstate+ndeath;j++){
       for(j=1; j<= nlstate; j++) /* vareij */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         for(h=0; h<=nhstepm; h++){            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            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); */
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          }
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       }        }
       }
     } /* End theta */      
       for(i=1; i<= nlstate; i++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */        s1=0;
         for(j=1; j<i; j++){
     for(h=0; h<=nhstepm; h++) /* veij */          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       for(j=1; j<=nlstate;j++)          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         for(theta=1; theta <=npar; theta++)        }
           trgradg[h][j][theta]=gradg[h][theta][j];        for(j=i+1; j<=nlstate+ndeath; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       for(theta=1; theta <=npar; theta++)        }
         trgradgp[j][theta]=gradgp[theta][j];        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         ps[i][i]=1./(s1+1.);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        /* Computing other pijs */
     for(i=1;i<=nlstate;i++)        for(j=1; j<i; j++)
       for(j=1;j<=nlstate;j++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
         vareij[i][j][(int)age] =0.;        for(j=i+1; j<=nlstate+ndeath; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
     for(h=0;h<=nhstepm;h++){        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for(k=0;k<=nhstepm;k++){      } /* end i */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(i=1;i<=nlstate;i++)        for(jj=1; jj<= nlstate+ndeath; jj++){
           for(j=1;j<=nlstate;j++)          ps[ii][jj]=0;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          ps[ii][ii]=1;
       }        }
     }      }
       
     /* pptj */      
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     for(j=nlstate+1;j<=nlstate+ndeath;j++)      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       for(i=nlstate+1;i<=nlstate+ndeath;i++)      /*   } */
         varppt[j][i]=doldmp[j][i];      /*   printf("\n "); */
     /* end ppptj */      /* } */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);        /* printf("\n ");printf("%lf ",cov[2]);*/
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);      /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
     if (popbased==1) {        goto end;*/
       for(i=1; i<=nlstate;i++)      return ps;
         prlim[i][i]=probs[(int)age][i][ij];  }
     }  
      /**************** Product of 2 matrices ******************/
     /* This for computing force of mortality (h=1)as a weighted average */  
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       for(i=1; i<= nlstate; i++)  {
         gmp[j] += prlim[i][i]*p3mat[i][j][1];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     }           b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* end force of mortality */    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);       a pointer to pointers identical to out */
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    int i, j, k;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));    for(i=nrl; i<= nrh; i++)
       for(i=1; i<=nlstate;i++){      for(k=ncolol; k<=ncoloh; k++){
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);        out[i][k]=0.;
       }        for(j=ncl; j<=nch; j++)
     }          out[i][k] +=in[i][j]*b[j][k];
     fprintf(ficresprobmorprev,"\n");      }
     return out;
     fprintf(ficresvij,"%.0f ",age );  }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  /************* Higher Matrix Product ***************/
       }  
     fprintf(ficresvij,"\n");  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     free_matrix(gp,0,nhstepm,1,nlstate);  {
     free_matrix(gm,0,nhstepm,1,nlstate);    /* Computes the transition matrix starting at age 'age' over 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);       'nhstepm*hstepm*stepm' months (i.e. until
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       nhstepm*hstepm matrices. 
   } /* End age */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   free_vector(gpp,nlstate+1,nlstate+ndeath);       (typically every 2 years instead of every month which is too big 
   free_vector(gmp,nlstate+1,nlstate+ndeath);       for the memory).
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);       Model is determined by parameters x and covariates have to be 
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/       included manually here. 
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");  
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */       */
   fprintf(ficgp,"\n set log y; set nolog 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);    int i, j, d, h, k;
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);    double **out, cov[NCOVMAX+1];
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);    double **newm;
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    double agexact;
   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.png\";replot;",digitp,digit);    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
   free_vector(xp,1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(doldm,1,nlstate,1,nlstate);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   free_matrix(dnewm,1,nlstate,1,npar);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      }
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    for(h=1; h <=nhstepm; h++){
   fclose(ficresprobmorprev);      for(d=1; d <=hstepm; d++){
   fclose(ficgp);        newm=savm;
   fclose(fichtm);        /* Covariates have to be included here again */
         cov[1]=1.;
 }        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         cov[2]=agexact;
 /************ Variance of prevlim ******************/        if(nagesqr==1)
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          cov[3]= agexact*agexact;
 {        for (k=1; k<=cptcovn;k++) 
   /* Variance of prevalence limit */          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
   double **newm;          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   double **dnewm,**doldm;          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
   int i, j, nhstepm, hstepm;        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   int k, cptcode;          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double *xp;  
   double *gp, *gm;  
   double **gradg, **trgradg;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double age,agelim;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   int theta;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                         pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");        savm=oldm;
   fprintf(ficresvpl,"# Age");        oldm=newm;
   for(i=1; i<=nlstate;i++)      }
       fprintf(ficresvpl," %1d-%1d",i,i);      for(i=1; i<=nlstate+ndeath; i++)
   fprintf(ficresvpl,"\n");        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
   xp=vector(1,npar);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   dnewm=matrix(1,nlstate,1,npar);        }
   doldm=matrix(1,nlstate,1,nlstate);      /*printf("h=%d ",h);*/
      } /* end h */
   hstepm=1*YEARM; /* Every year of age */  /*     printf("\n H=%d \n",h); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    return po;
   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 */  #ifdef NLOPT
     if (stepm >= YEARM) hstepm=1;    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double fret;
     gradg=matrix(1,npar,1,nlstate);    double *xt;
     gp=vector(1,nlstate);    int j;
     gm=vector(1,nlstate);    myfunc_data *d2 = (myfunc_data *) pd;
   /* xt = (p1-1); */
     for(theta=1; theta <=npar; theta++){    xt=vector(1,n); 
       for(i=1; i<=npar; i++){ /* Computes gradient */    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
       for(i=1;i<=nlstate;i++)    printf("Function = %.12lf ",fret);
         gp[i] = prlim[i][i];    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
        printf("\n");
       for(i=1; i<=npar; i++) /* Computes gradient */   free_vector(xt,1,n);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    return fret;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
       for(i=1;i<=nlstate;i++)  #endif
         gm[i] = prlim[i][i];  
   /*************** log-likelihood *************/
       for(i=1;i<=nlstate;i++)  double func( double *x)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  {
     } /* End theta */    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     trgradg =matrix(1,nlstate,1,npar);    double **out;
     double sw; /* Sum of weights */
     for(j=1; j<=nlstate;j++)    double lli; /* Individual log likelihood */
       for(theta=1; theta <=npar; theta++)    int s1, s2;
         trgradg[j][theta]=gradg[theta][j];    double bbh, survp;
     long ipmx;
     for(i=1;i<=nlstate;i++)    double agexact;
       varpl[i][(int)age] =0.;    /*extern weight */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    /* We are differentiating ll according to initial status */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(i=1;i<=nlstate;i++)    /*for(i=1;i<imx;i++) 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      printf(" %d\n",s[4][i]);
     */
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    ++countcallfunc;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");    cov[1]=1.;
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);    if(mle==1){
   } /* End age */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /* Computes the values of the ncovmodel covariates of the model
   free_vector(xp,1,npar);           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   free_matrix(doldm,1,nlstate,1,npar);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   free_matrix(dnewm,1,nlstate,1,nlstate);           to be observed in j being in i according to the model.
          */
 }        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
             cov[2+nagesqr+k]=covar[Tvar[k]][i];
 /************ 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)        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
 {           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   int i, j=0,  i1, k1, l1, t, tj;           has been calculated etc */
   int k2, l2, j1,  z1;        for(mi=1; mi<= wav[i]-1; mi++){
   int k=0,l, cptcode;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int first=1, first1;            for (j=1;j<=nlstate+ndeath;j++){
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **dnewm,**doldm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *xp;            }
   double *gp, *gm;          for(d=0; d<dh[mi][i]; d++){
   double **gradg, **trgradg;            newm=savm;
   double **mu;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double age,agelim, cov[NCOVMAX];            cov[2]=agexact;
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */            if(nagesqr==1)
   int theta;              cov[3]= agexact*agexact;
   char fileresprob[FILENAMELENGTH];            for (kk=1; kk<=cptcovage;kk++) {
   char fileresprobcov[FILENAMELENGTH];              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
   char fileresprobcor[FILENAMELENGTH];            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***varpij;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   strcpy(fileresprob,"prob");            oldm=newm;
   strcat(fileresprob,fileres);          } /* end mult */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        
     printf("Problem with resultfile: %s\n", fileresprob);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);          /* But now since version 0.9 we anticipate for bias at large stepm.
   }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   strcpy(fileresprobcov,"probcov");           * (in months) between two waves is not a multiple of stepm, we rounded to 
   strcat(fileresprobcov,fileres);           * the nearest (and in case of equal distance, to the lowest) interval but now
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     printf("Problem with resultfile: %s\n", fileresprobcov);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   strcpy(fileresprobcor,"probcor");           * -stepm/2 to stepm/2 .
   strcat(fileresprobcor,fileres);           * For stepm=1 the results are the same as for previous versions of Imach.
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {           * For stepm > 1 the results are less biased than in previous versions. 
     printf("Problem with resultfile: %s\n", fileresprobcor);           */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          /* bias bh is positive if real duration
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);           * is higher than the multiple of stepm and negative otherwise.
   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);          /* 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(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);          if( s2 > nlstate){ 
              /* i.e. if s2 is a death state and if the date of death is known 
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");               then the contribution to the likelihood is the probability to 
   fprintf(ficresprob,"# Age");               die between last step unit time and current  step unit time, 
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");               which is also equal to probability to die before dh 
   fprintf(ficresprobcov,"# Age");               minus probability to die before dh-stepm . 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");               In version up to 0.92 likelihood was computed
   fprintf(ficresprobcov,"# Age");          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
   for(i=1; i<=nlstate;i++)          to consider that at each interview the state was recorded
     for(j=1; j<=(nlstate+ndeath);j++){          (healthy, disable or death) and IMaCh was corrected; but when we
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          introduced the exact date of death then we should have modified
       fprintf(ficresprobcov," p%1d-%1d ",i,j);          the contribution of an exact death to the likelihood. This new
       fprintf(ficresprobcor," p%1d-%1d ",i,j);          contribution is smaller and very dependent of the step unit
     }            stepm. It is no more the probability to die between last interview
   fprintf(ficresprob,"\n");          and month of death but the probability to survive from last
   fprintf(ficresprobcov,"\n");          interview up to one month before death multiplied by the
   fprintf(ficresprobcor,"\n");          probability to die within a month. Thanks to Chris
   xp=vector(1,npar);          Jackson for correcting this bug.  Former versions increased
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          mortality artificially. The bad side is that we add another loop
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));          which slows down the processing. The difference can be up to 10%
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);          lower mortality.
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);            */
   first=1;          /* If, at the beginning of the maximization mostly, the
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {             cumulative probability or probability to be dead is
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);             constant (ie = 1) over time d, the difference is equal to
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);             0.  out[s1][3] = savm[s1][3]: probability, being at state
     exit(0);             s1 at precedent wave, to be dead a month before current
   }             wave is equal to probability, being at state s1 at
   else{             precedent wave, to be dead at mont of the current
     fprintf(ficgp,"\n# Routine varprob");             wave. Then the observed probability (that this person died)
   }             is null according to current estimated parameter. In fact,
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {             it should be very low but not zero otherwise the log go to
     printf("Problem with html file: %s\n", optionfilehtm);             infinity.
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);          */
     exit(0);  /* #ifdef INFINITYORIGINAL */
   }  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   else{  /* #else */
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
     fprintf(fichtm,"\n");  /*          lli=log(mytinydouble); */
   /*        else */
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");  /* #endif */
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix 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> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");              lli=log(out[s1][s2] - savm[s1][s2]);
   
   }          } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   cov[1]=1;            /*survp += out[s1][j]; */
   tj=cptcoveff;            lli= log(survp);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}          }
   j1=0;          
   for(t=1; t<=tj;t++){          else if  (s2==-4) { 
     for(i1=1; i1<=ncodemax[t];i1++){            for (j=3,survp=0. ; j<=nlstate; j++)  
       j1++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                  lli= log(survp); 
       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]]);          else if  (s2==-5) { 
         fprintf(ficresprob, "**********\n#");            for (j=1,survp=0. ; j<=2; j++)  
         fprintf(ficresprobcov, "\n#********** Variable ");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            lli= log(survp); 
         fprintf(ficresprobcov, "**********\n#");          } 
                  
         fprintf(ficgp, "\n#********** Variable ");          else{
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         fprintf(ficgp, "**********\n#");            /*  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 */
                  } 
                  /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          /*if(lli ==000.0)*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");          ipmx +=1;
                  sw += weight[i];
         fprintf(ficresprobcor, "\n#********** Variable ");              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          /* 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]); */
                /* } */
       for (age=bage; age<=fage; age ++){        } /* end of wave */
         cov[2]=age;      } /* end of individual */
         for (k=1; k<=cptcovn;k++) {    }  else if(mle==2){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for(mi=1; mi<= wav[i]-1; mi++){
         for (k=1; k<=cptcovprod;k++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            for (j=1;j<=nlstate+ndeath;j++){
                      oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);            }
         gp=vector(1,(nlstate)*(nlstate+ndeath));          for(d=0; d<=dh[mi][i]; d++){
         gm=vector(1,(nlstate)*(nlstate+ndeath));            newm=savm;
                agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(theta=1; theta <=npar; theta++){            cov[2]=agexact;
           for(i=1; i<=npar; i++)            if(nagesqr==1)
             xp[i] = x[i] + (i==theta ?delti[theta]:0);              cov[3]= agexact*agexact;
                      for (kk=1; kk<=cptcovage;kk++) {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                      }
           k=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(i=1; i<= (nlstate); i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             for(j=1; j<=(nlstate+ndeath);j++){            savm=oldm;
               k=k+1;            oldm=newm;
               gp[k]=pmmij[i][j];          } /* end mult */
             }        
           }          s1=s[mw[mi][i]][i];
                    s2=s[mw[mi+1][i]][i];
           for(i=1; i<=npar; i++)          bbh=(double)bh[mi][i]/(double)stepm; 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
              ipmx +=1;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          sw += weight[i];
           k=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(i=1; i<=(nlstate); i++){        } /* end of wave */
             for(j=1; j<=(nlstate+ndeath);j++){      } /* end of individual */
               k=k+1;    }  else if(mle==3){  /* exponential inter-extrapolation */
               gm[k]=pmmij[i][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             }        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
           }        for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)            for (j=1;j<=nlstate+ndeath;j++){
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)          for(d=0; d<dh[mi][i]; d++){
           for(theta=1; theta <=npar; theta++)            newm=savm;
             trgradg[j][theta]=gradg[theta][j];            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                    cov[2]=agexact;
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);            if(nagesqr==1)
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);              cov[3]= agexact*agexact;
                    for (kk=1; kk<=cptcovage;kk++) {
         pmij(pmmij,cov,ncovmodel,x,nlstate);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                    }
         k=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(i=1; i<=(nlstate); i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(j=1; j<=(nlstate+ndeath);j++){            savm=oldm;
             k=k+1;            oldm=newm;
             mu[k][(int) age]=pmmij[i][j];          } /* end mult */
           }        
         }          s1=s[mw[mi][i]][i];
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)          s2=s[mw[mi+1][i]][i];
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)          bbh=(double)bh[mi][i]/(double)stepm; 
             varpij[i][j][(int)age] = doldm[i][j];          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
         /*printf("\n%d ",(int)age);          sw += weight[i];
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        } /* end of wave */
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      } /* end of individual */
      }*/    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficresprob,"\n%d ",(int)age);        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
         fprintf(ficresprobcov,"\n%d ",(int)age);        for(mi=1; mi<= wav[i]-1; mi++){
         fprintf(ficresprobcor,"\n%d ",(int)age);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){            }
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);          for(d=0; d<dh[mi][i]; d++){
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);            newm=savm;
         }            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
         i=0;            cov[2]=agexact;
         for (k=1; k<=(nlstate);k++){            if(nagesqr==1)
           for (l=1; l<=(nlstate+ndeath);l++){              cov[3]= agexact*agexact;
             i=i++;            for (kk=1; kk<=cptcovage;kk++) {
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);            }
             for (j=1; j<=i;j++){          
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             }            savm=oldm;
           }            oldm=newm;
         }/* end of loop for state */          } /* end mult */
       } /* end of loop for age */        
           s1=s[mw[mi][i]][i];
       /* Confidence intervalle of pij  */          s2=s[mw[mi+1][i]][i];
       /*          if( s2 > nlstate){ 
       fprintf(ficgp,"\nset noparametric;unset label");            lli=log(out[s1][s2] - savm[s1][s2]);
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");          }else{
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       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);          ipmx +=1;
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);          sw += weight[i];
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       */  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/      } /* end of individual */
       first1=1;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (k2=1; k2<=(nlstate);k2++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (l2=1; l2<=(nlstate+ndeath);l2++){        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
           if(l2==k2) continue;        for(mi=1; mi<= wav[i]-1; mi++){
           j=(k2-1)*(nlstate+ndeath)+l2;          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (k1=1; k1<=(nlstate);k1++){            for (j=1;j<=nlstate+ndeath;j++){
             for (l1=1; l1<=(nlstate+ndeath);l1++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(l1==k1) continue;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               i=(k1-1)*(nlstate+ndeath)+l1;            }
               if(i<=j) continue;          for(d=0; d<dh[mi][i]; d++){
               for (age=bage; age<=fage; age ++){            newm=savm;
                 if ((int)age %5==0){            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;            cov[2]=agexact;
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;            if(nagesqr==1)
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;              cov[3]= agexact*agexact;
                   mu1=mu[i][(int) age]/stepm*YEARM ;            for (kk=1; kk<=cptcovage;kk++) {
                   mu2=mu[j][(int) age]/stepm*YEARM;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   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.;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   /* Eigen vectors */            savm=oldm;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));            oldm=newm;
                   /*v21=sqrt(1.-v11*v11); *//* error */          } /* end mult */
                   v21=(lc1-v1)/cv12*v11;        
                   v12=-v21;          s1=s[mw[mi][i]][i];
                   v22=v11;          s2=s[mw[mi+1][i]][i];
                   tnalp=v21/v11;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   if(first1==1){          ipmx +=1;
                     first1=0;          sw += weight[i];
                     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);          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(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);        } /* end of wave */
                   /*printf(fignu*/      } /* end of individual */
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    } /* End of if */
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   if(first==1){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                     first=0;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                     fprintf(ficgp,"\nset parametric;unset label");    return -l;
                     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\nset size 0.65,0.65");  
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);  /*************** log-likelihood *************/
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);  double funcone( double *x)
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);  {
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    /* Same as likeli but slower because of a lot of printf and if */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    int i, ii, j, k, mi, d, kk;
                     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",\    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    double **out;
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));    double lli; /* Individual log likelihood */
                   }else{    double llt;
                     first=0;    int s1, s2;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    double bbh, survp;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    double agexact;
                     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",\    /*extern weight */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    /* We are differentiating ll according to initial status */
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   }/* if first */    /*for(i=1;i<imx;i++) 
                 } /* age mod 5 */      printf(" %d\n",s[4][i]);
               } /* end loop age */    */
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);    cov[1]=1.;
               first=1;  
             } /*l12 */    for(k=1; k<=nlstate; k++) ll[k]=0.;
           } /* k12 */  
         } /*l1 */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }/* k1 */      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
     } /* loop covariates */      for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        for (ii=1;ii<=nlstate+ndeath;ii++)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          for (j=1;j<=nlstate+ndeath;j++){
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(d=0; d<dh[mi][i]; d++){
   }          newm=savm;
   free_vector(xp,1,npar);          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fclose(ficresprob);          cov[2]=agexact;
   fclose(ficresprobcov);          if(nagesqr==1)
   fclose(ficresprobcor);            cov[3]= agexact*agexact;
   fclose(ficgp);          for (kk=1; kk<=cptcovage;kk++) {
   fclose(fichtm);            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
 }          }
   
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 /******************* Printing html file ***********/          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   int lastpass, int stepm, int weightopt, char model[],\          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
                   int popforecast, int estepm ,\          savm=oldm;
                   double jprev1, double mprev1,double anprev1, \          oldm=newm;
                   double jprev2, double mprev2,double anprev2){        } /* end mult */
   int jj1, k1, i1, cpt;        
   /*char optionfilehtm[FILENAMELENGTH];*/        s1=s[mw[mi][i]][i];
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {        s2=s[mw[mi+1][i]][i];
     printf("Problem with %s \n",optionfilehtm), exit(0);        bbh=(double)bh[mi][i]/(double)stepm; 
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);        /* bias is positive if real duration
   }         * is higher than the multiple of stepm and negative otherwise.
          */
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n        if( s2 > nlstate && (mle <5) ){  /* Jackson */
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n          lli=log(out[s1][s2] - savm[s1][s2]);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        } else if  (s2==-2) {
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n          for (j=1,survp=0. ; j<=nlstate; j++) 
  - Life expectancies by age and initial health status (estepm=%2d months):            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
    <a href=\"e%s\">e%s</a> <br>\n</li>", \          lli= log(survp);
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");        } else if(mle==2){
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
  m=cptcoveff;        } else if(mle==3){  /* exponential inter-extrapolation */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          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 */
  jj1=0;          lli=log(out[s1][s2]); /* Original formula */
  for(k1=1; k1<=m;k1++){        } else{  /* mle=0 back to 1 */
    for(i1=1; i1<=ncodemax[k1];i1++){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      jj1++;          /*lli=log(out[s1][s2]); */ /* Original formula */
      if (cptcovn > 0) {        } /* End of if */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        ipmx +=1;
        for (cpt=1; cpt<=cptcoveff;cpt++)        sw += weight[i];
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        /*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){
      /* Pij */          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>   %11.6f %11.6f %11.6f ", \
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                      num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      /* Quasi-incidences */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            llt +=ll[k]*gipmx/gsw;
        /* Stable prevalence in each health state */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
        for(cpt=1; cpt<nlstate;cpt++){          }
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>          fprintf(ficresilk," %10.6f\n", -llt);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        }
        }      } /* end of wave */
      for(cpt=1; cpt<=nlstate;cpt++) {    } /* end of individual */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    if(globpr==0){ /* First time we count the contributions and weights */
 health expectancies in states (1) and (2): e%s%d.png<br>      gipmx=ipmx;
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      gsw=sw;
    } /* end i1 */    }
  }/* End k1 */    return -l;
  fprintf(fichtm,"</ul>");  }
   
   
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n  /*************** function likelione ***********/
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n  {
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    /* This routine should help understanding what is done with 
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n       the selection of individuals/waves and
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n       to check the exact contribution to the likelihood.
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n       Plotting could be done.
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);     */
     int k;
  if(popforecast==1) fprintf(fichtm,"\n  
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    if(*globpri !=0){ /* Just counts and sums, no printings */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      strcpy(fileresilk,"ilk"); 
         <br>",fileres,fileres,fileres,fileres);      strcat(fileresilk,fileres);
  else      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
    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);        printf("Problem with resultfile: %s\n", fileresilk);
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
  m=cptcoveff;      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");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      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]); */
  jj1=0;      for(k=1; k<=nlstate; k++) 
  for(k1=1; k1<=m;k1++){        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
    for(i1=1; i1<=ncodemax[k1];i1++){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      jj1++;    }
      if (cptcovn > 0) {  
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    *fretone=(*funcone)(p);
        for (cpt=1; cpt<=cptcoveff;cpt++)    if(*globpri !=0){
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      fclose(ficresilk);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
      }      fflush(fichtm); 
      for(cpt=1; cpt<=nlstate;cpt++) {    } 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    return;
 interval) in state (%d): v%s%d%d.png <br>  }
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }  
    } /* end i1 */  /*********** Maximum Likelihood Estimation ***************/
  }/* End k1 */  
  fprintf(fichtm,"</ul>");  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 fclose(fichtm);  {
 }    int i,j, iter=0;
     double **xi;
 /******************* Gnuplot file **************/    double fret;
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
   int ng;  #ifdef NLOPT
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    int creturn;
     printf("Problem with file %s",optionfilegnuplot);    nlopt_opt opt;
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);    /* 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;
     double minf; /* the minimum objective value, upon return */
 #ifdef windows    double * p1; /* Shifted parameters from 0 instead of 1 */
     fprintf(ficgp,"cd \"%s\" \n",pathc);    myfunc_data dinst, *d = &dinst;
 #endif  #endif
 m=pow(2,cptcoveff);  
    
  /* 1eme*/    xi=matrix(1,npar,1,npar);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (i=1;i<=npar;i++)
    for (k1=1; k1<= m ; k1 ++) {      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
 #ifdef windows    printf("Powell\n");  fprintf(ficlog,"Powell\n");
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    strcpy(filerespow,"pow"); 
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    strcat(filerespow,fileres);
 #endif    if((ficrespow=fopen(filerespow,"w"))==NULL) {
 #ifdef unix      printf("Problem with resultfile: %s\n", filerespow);
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    }
 #endif    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {      for(j=1;j<=nlstate+ndeath;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficrespow,"\n");
 }  #ifdef POWELL
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    powell(p,xi,npar,ftol,&iter,&fret,func);
     for (i=1; i<= nlstate ; i ++) {  #endif
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  #ifdef NLOPT
 }  #ifdef NEWUOA
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
      for (i=1; i<= nlstate ; i ++) {  #else
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  #endif
 }      lb=vector(0,npar-1);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
 #ifdef unix    nlopt_set_lower_bounds(opt, lb);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    nlopt_set_initial_step1(opt, 0.1);
 #endif    
    }    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   }    d->function = func;
   /*2 eme*/    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     nlopt_set_min_objective(opt, myfunc, d);
   for (k1=1; k1<= m ; k1 ++) {    nlopt_set_xtol_rel(opt, ftol);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      printf("nlopt failed! %d\n",creturn); 
        }
     for (i=1; i<= nlstate+1 ; i ++) {    else {
       k=2*i;      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       for (j=1; j<= nlstate+1 ; j ++) {      iter=1; /* not equal */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    nlopt_destroy(opt);
 }    #endif
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    free_matrix(xi,1,npar,1,npar);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    fclose(ficrespow);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
       for (j=1; j<= nlstate+1 ; j ++) {    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    }
       fprintf(ficgp,"\" t\"\" w l 0,");  
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  /**** Computes Hessian and covariance matrix ***/
       for (j=1; j<= nlstate+1 ; j ++) {  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  {
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double  **a,**y,*x,pd;
 }      double **hess;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    int i, j;
       else fprintf(ficgp,"\" t\"\" w l 0,");    int *indx;
     }  
   }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
      double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   /*3eme*/    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
   for (k1=1; k1<= m ; k1 ++) {    double gompertz(double p[]);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    hess=matrix(1,npar,1,npar);
       k=2+nlstate*(2*cpt-2);  
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    printf("\nCalculation of the hessian matrix. Wait...\n");
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    for (i=1;i<=npar;i++){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      printf("%d",i);fflush(stdout);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      fprintf(ficlog,"%d",i);fflush(ficlog);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);     
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      
       /*  printf(" %f ",p[i]);
 */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       for (i=1; i< nlstate ; i ++) {    }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    
     for (i=1;i<=npar;i++) {
       }      for (j=1;j<=npar;j++)  {
     }        if (j>i) { 
   }          printf(".%d%d",i,j);fflush(stdout);
            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   /* CV preval stat */          hess[i][j]=hessij(p,delti,i,j,func,npar);
     for (k1=1; k1<= m ; k1 ++) {          
     for (cpt=1; cpt<nlstate ; cpt ++) {          hess[j][i]=hess[i][j];    
       k=3;          /*printf(" %lf ",hess[i][j]);*/
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      }
     }
       for (i=1; i< nlstate ; i ++)    printf("\n");
         fprintf(ficgp,"+$%d",k+i+1);    fprintf(ficlog,"\n");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
          printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       l=3+(nlstate+ndeath)*cpt;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    
       for (i=1; i< nlstate ; i ++) {    a=matrix(1,npar,1,npar);
         l=3+(nlstate+ndeath)*cpt;    y=matrix(1,npar,1,npar);
         fprintf(ficgp,"+$%d",l+i+1);    x=vector(1,npar);
       }    indx=ivector(1,npar);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   }      ludcmp(a,npar,indx,&pd);
    
   /* proba elementaires */    for (j=1;j<=npar;j++) {
    for(i=1,jk=1; i <=nlstate; i++){      for (i=1;i<=npar;i++) x[i]=0;
     for(k=1; k <=(nlstate+ndeath); k++){      x[j]=1;
       if (k != i) {      lubksb(a,npar,indx,x);
         for(j=1; j <=ncovmodel; j++){      for (i=1;i<=npar;i++){ 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        matcov[i][j]=x[i];
           jk++;      }
           fprintf(ficgp,"\n");    }
         }  
       }    printf("\n#Hessian matrix#\n");
     }    fprintf(ficlog,"\n#Hessian matrix#\n");
    }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        printf("%.3e ",hess[i][j]);
      for(jk=1; jk <=m; jk++) {        fprintf(ficlog,"%.3e ",hess[i][j]);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);      }
        if (ng==2)      printf("\n");
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");      fprintf(ficlog,"\n");
        else    }
          fprintf(ficgp,"\nset title \"Probability\"\n");  
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    /* Recompute Inverse */
        i=1;    for (i=1;i<=npar;i++)
        for(k2=1; k2<=nlstate; k2++) {      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
          k3=i;    ludcmp(a,npar,indx,&pd);
          for(k=1; k<=(nlstate+ndeath); k++) {  
            if (k != k2){    /*  printf("\n#Hessian matrix recomputed#\n");
              if(ng==2)  
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    for (j=1;j<=npar;j++) {
              else      for (i=1;i<=npar;i++) x[i]=0;
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      x[j]=1;
              ij=1;      lubksb(a,npar,indx,x);
              for(j=3; j <=ncovmodel; j++) {      for (i=1;i<=npar;i++){ 
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        y[i][j]=x[i];
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        printf("%.3e ",y[i][j]);
                  ij++;        fprintf(ficlog,"%.3e ",y[i][j]);
                }      }
                else      printf("\n");
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      fprintf(ficlog,"\n");
              }    }
              fprintf(ficgp,")/(1");    */
                
              for(k1=1; k1 <=nlstate; k1++){      free_matrix(a,1,npar,1,npar);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    free_matrix(y,1,npar,1,npar);
                ij=1;    free_vector(x,1,npar);
                for(j=3; j <=ncovmodel; j++){    free_ivector(indx,1,npar);
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    free_matrix(hess,1,npar,1,npar);
                    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]]);  /*************** hessian matrix ****************/
                }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
                fprintf(ficgp,")");  {
              }    int i;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    int l=1, lmax=20;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    double k1,k2;
              i=i+ncovmodel;    double p2[MAXPARM+1]; /* identical to x */
            }    double res;
          } /* end k */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
        } /* end k2 */    double fx;
      } /* end jk */    int k=0,kmax=10;
    } /* end ng */    double l1;
    fclose(ficgp);  
 }  /* end gnuplot */    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
 /*************** Moving average **************/      l1=pow(10,l);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
   int i, cpt, cptcod;        delt = delta*(l1*k);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        p2[theta]=x[theta] +delt;
       for (i=1; i<=nlstate;i++)        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        p2[theta]=x[theta]-delt;
           mobaverage[(int)agedeb][i][cptcod]=0.;        k2=func(p2)-fx;
            /*res= (k1-2.0*fx+k2)/delt/delt; */
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       for (i=1; i<=nlstate;i++){        
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  #ifdef DEBUGHESS
           for (cpt=0;cpt<=4;cpt++){        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);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           }  #endif
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       }          k=kmax;
     }        }
            else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 }          k=kmax; l=lmax*10;
         }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 /************** Forecasting ******************/          delts=delt;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        }
        }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    }
   int *popage;    delti[theta]=delts;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    return res; 
   double *popeffectif,*popcount;    
   double ***p3mat;  }
   char fileresf[FILENAMELENGTH];  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  agelim=AGESUP;  {
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    int i;
     int l=1, lmax=20;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double k1,k2,k3,k4,res,fx;
      double p2[MAXPARM+1];
      int k;
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);    fx=func(x);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    for (k=1; k<=2; k++) {
     printf("Problem with forecast resultfile: %s\n", fileresf);      for (i=1;i<=npar;i++) p2[i]=x[i];
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);      p2[thetai]=x[thetai]+delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   printf("Computing forecasting: result on file '%s' \n", fileresf);      k1=func(p2)-fx;
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    
       p2[thetai]=x[thetai]+delti[thetai]/k;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
   if (mobilav==1) {    
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      p2[thetai]=x[thetai]-delti[thetai]/k;
     movingaverage(agedeb, fage, ageminpar, mobaverage);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   }      k3=func(p2)-fx;
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;      p2[thetai]=x[thetai]-delti[thetai]/k;
   if (stepm<=12) stepsize=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k4=func(p2)-fx;
   agelim=AGESUP;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    #ifdef DEBUG
   hstepm=1;      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   hstepm=hstepm/stepm;      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);
   yp1=modf(dateintmean,&yp);  #endif
   anprojmean=yp;    }
   yp2=modf((yp1*12),&yp);    return res;
   mprojmean=yp;  }
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;  /************** Inverse of matrix **************/
   if(jprojmean==0) jprojmean=1;  void ludcmp(double **a, int n, int *indx, double *d) 
   if(mprojmean==0) jprojmean=1;  { 
      int i,imax,j,k; 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    double big,dum,sum,temp; 
      double *vv; 
   for(cptcov=1;cptcov<=i2;cptcov++){   
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    vv=vector(1,n); 
       k=k+1;    *d=1.0; 
       fprintf(ficresf,"\n#******");    for (i=1;i<=n;i++) { 
       for(j=1;j<=cptcoveff;j++) {      big=0.0; 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for (j=1;j<=n;j++) 
       }        if ((temp=fabs(a[i][j])) > big) big=temp; 
       fprintf(ficresf,"******\n");      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       fprintf(ficresf,"# StartingAge FinalAge");      vv[i]=1.0/big; 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    } 
          for (j=1;j<=n;j++) { 
            for (i=1;i<j;i++) { 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        sum=a[i][j]; 
         fprintf(ficresf,"\n");        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          a[i][j]=sum; 
       } 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      big=0.0; 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for (i=j;i<=n;i++) { 
           nhstepm = nhstepm/hstepm;        sum=a[i][j]; 
                  for (k=1;k<j;k++) 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          sum -= a[i][k]*a[k][j]; 
           oldm=oldms;savm=savms;        a[i][j]=sum; 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          if ( (dum=vv[i]*fabs(sum)) >= big) { 
                  big=dum; 
           for (h=0; h<=nhstepm; h++){          imax=i; 
             if (h==(int) (calagedate+YEARM*cpt)) {        } 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      } 
             }      if (j != imax) { 
             for(j=1; j<=nlstate+ndeath;j++) {        for (k=1;k<=n;k++) { 
               kk1=0.;kk2=0;          dum=a[imax][k]; 
               for(i=1; i<=nlstate;i++) {                        a[imax][k]=a[j][k]; 
                 if (mobilav==1)          a[j][k]=dum; 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        } 
                 else {        *d = -(*d); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        vv[imax]=vv[j]; 
                 }      } 
                      indx[j]=imax; 
               }      if (a[j][j] == 0.0) a[j][j]=TINY; 
               if (h==(int)(calagedate+12*cpt)){      if (j != n) { 
                 fprintf(ficresf," %.3f", kk1);        dum=1.0/(a[j][j]); 
                                for (i=j+1;i<=n;i++) a[i][j] *= dum; 
               }      } 
             }    } 
           }    free_vector(vv,1,n);  /* Doesn't work */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  ;
         }  } 
       }  
     }  void lubksb(double **a, int n, int *indx, double b[]) 
   }  { 
            int i,ii=0,ip,j; 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double sum; 
    
   fclose(ficresf);    for (i=1;i<=n;i++) { 
 }      ip=indx[i]; 
 /************** Forecasting ******************/      sum=b[ip]; 
 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){      b[ip]=b[i]; 
        if (ii) 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   int *popage;      else if (sum) ii=i; 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      b[i]=sum; 
   double *popeffectif,*popcount;    } 
   double ***p3mat,***tabpop,***tabpopprev;    for (i=n;i>=1;i--) { 
   char filerespop[FILENAMELENGTH];      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      b[i]=sum/a[i][i]; 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    } 
   agelim=AGESUP;  } 
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  
    void pstamp(FILE *fichier)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  {
      fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
    }
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);  /************ Frequencies ********************/
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  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[])
     printf("Problem with forecast resultfile: %s\n", filerespop);  {  /* Some frequencies */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);    
   }    int i, m, jk, j1, bool, z1,j;
   printf("Computing forecasting: result on file '%s' \n", filerespop);    int first;
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);    double ***freq; /* Frequencies */
     double *pp, **prop;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
   if (mobilav==1) {    
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    pp=vector(1,nlstate);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   }    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   if (stepm<=12) stepsize=1;      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   agelim=AGESUP;      exit(0);
      }
   hstepm=1;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   hstepm=hstepm/stepm;    j1=0;
      
   if (popforecast==1) {    j=cptcoveff;
     if((ficpop=fopen(popfile,"r"))==NULL) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       printf("Problem with population file : %s\n",popfile);exit(0);  
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);    first=1;
     }  
     popage=ivector(0,AGESUP);    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
     popeffectif=vector(0,AGESUP);    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
     popcount=vector(0,AGESUP);    /*    j1++; */
        for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
     i=1;          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          scanf("%d", i);*/
            for (i=-5; i<=nlstate+ndeath; i++)  
     imx=i;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            for(m=iagemin; m <= iagemax+3; m++)
   }              freq[i][jk][m]=0;
         
   for(cptcov=1;cptcov<=i2;cptcov++){        for (i=1; i<=nlstate; i++)  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for(m=iagemin; m <= iagemax+3; m++)
       k=k+1;            prop[i][m]=0;
       fprintf(ficrespop,"\n#******");        
       for(j=1;j<=cptcoveff;j++) {        dateintsum=0;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        k2cpt=0;
       }        for (i=1; i<=imx; i++) {
       fprintf(ficrespop,"******\n");          bool=1;
       fprintf(ficrespop,"# Age");          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            for (z1=1; z1<=cptcoveff; z1++)       
       if (popforecast==1)  fprintf(ficrespop," [Population]");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                        /* Tests if the value of each of the covariates of i is equal to filter j1 */
       for (cpt=0; cpt<=0;cpt++) {                bool=0;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                  /* 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],
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
           nhstepm = nhstepm/hstepm;              } 
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   
           oldm=oldms;savm=savms;          if (bool==1){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(m=firstpass; m<=lastpass; m++){
                      k2=anint[m][i]+(mint[m][i]/12.);
           for (h=0; h<=nhstepm; h++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
             if (h==(int) (calagedate+YEARM*cpt)) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
             for(j=1; j<=nlstate+ndeath;j++) {                if (m<lastpass) {
               kk1=0.;kk2=0;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
               for(i=1; i<=nlstate;i++) {                                freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 if (mobilav==1)                }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                
                 else {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                  dateintsum=dateintsum+k2;
                 }                  k2cpt++;
               }                }
               if (h==(int)(calagedate+12*cpt)){                /*}*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;            }
                   /*fprintf(ficrespop," %.3f", kk1);          }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        } /* end i */
               }         
             }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             for(i=1; i<=nlstate;i++){        pstamp(ficresp);
               kk1=0.;        if  (cptcovn>0) {
                 for(j=1; j<=nlstate;j++){          fprintf(ficresp, "\n#********** Variable "); 
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                 }          fprintf(ficresp, "**********\n#");
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          fprintf(ficlog, "\n#********** Variable "); 
             }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficlog, "**********\n#");
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for(i=1; i<=nlstate;i++) 
           }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresp, "\n");
         }        
       }        for(i=iagemin; i <= iagemax+3; i++){
            if(i==iagemax+3){
   /******/            fprintf(ficlog,"Total");
           }else{
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            if(first==1){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                first=0;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              printf("See log file for details...\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            }
           nhstepm = nhstepm/hstepm;            fprintf(ficlog,"Age %d", i);
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(jk=1; jk <=nlstate ; jk++){
           oldm=oldms;savm=savms;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                pp[jk] += freq[jk][m][i]; 
           for (h=0; h<=nhstepm; h++){          }
             if (h==(int) (calagedate+YEARM*cpt)) {          for(jk=1; jk <=nlstate ; jk++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            for(m=-1, pos=0; m <=0 ; m++)
             }              pos += freq[jk][m][i];
             for(j=1; j<=nlstate+ndeath;j++) {            if(pp[jk]>=1.e-10){
               kk1=0.;kk2=0;              if(first==1){
               for(i=1; i<=nlstate;i++) {                              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  }
               }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            }else{
             }              if(first==1)
           }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         }            }
       }          }
    }  
   }          for(jk=1; jk <=nlstate ; jk++){
              for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              pp[jk] += freq[jk][m][i];
           }       
   if (popforecast==1) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     free_ivector(popage,0,AGESUP);            pos += pp[jk];
     free_vector(popeffectif,0,AGESUP);            posprop += prop[jk][i];
     free_vector(popcount,0,AGESUP);          }
   }          for(jk=1; jk <=nlstate ; jk++){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if(pos>=1.e-5){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if(first==1)
   fclose(ficrespop);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
 /***********************************************/              if(first==1)
 /**************** Main Program *****************/                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 /***********************************************/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 int main(int argc, char *argv[])            if( i <= iagemax){
 {              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                /*probs[i][jk][j1]= pp[jk]/pos;*/
   double agedeb, agefin,hf;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              }
               else
   double fret;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double **xi,tmp,delta;            }
           }
   double dum; /* Dummy variable */          
   double ***p3mat;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   int *indx;            for(m=-1; m <=nlstate+ndeath; m++)
   char line[MAXLINE], linepar[MAXLINE];              if(freq[jk][m][i] !=0 ) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];              if(first==1)
   int firstobs=1, lastobs=10;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   int sdeb, sfin; /* Status at beginning and end */                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   int c,  h , cpt,l;              }
   int ju,jl, mi;          if(i <= iagemax)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            fprintf(ficresp,"\n");
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          if(first==1)
   int mobilav=0,popforecast=0;            printf("Others in log...\n");
   int hstepm, nhstepm;          fprintf(ficlog,"\n");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        }
         /*}*/
   double bage, fage, age, agelim, agebase;    }
   double ftolpl=FTOL;    dateintmean=dateintsum/k2cpt; 
   double **prlim;   
   double *severity;    fclose(ficresp);
   double ***param; /* Matrix of parameters */    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   double  *p;    free_vector(pp,1,nlstate);
   double **matcov; /* Matrix of covariance */    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   double ***delti3; /* Scale */    /* End of Freq */
   double *delti; /* Scale */  }
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  /************ Prevalence ********************/
   double *epj, vepp;  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)
   double kk1, kk2;  {  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
   char *alph[]={"a","a","b","c","d","e"}, str[4];    */
    
     int i, m, jk, j1, bool, z1,j;
   char z[1]="c", occ;  
 #include <sys/time.h>    double **prop;
 #include <time.h>    double posprop; 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double  y2; /* in fractional years */
      int iagemin, iagemax;
   /* long total_usecs;    int first; /** to stop verbosity which is redirected to log file */
   struct timeval start_time, end_time;  
      iagemin= (int) agemin;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    iagemax= (int) agemax;
   getcwd(pathcd, size);    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
   printf("\n%s",version);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if(argc <=1){    j1=0;
     printf("\nEnter the parameter file name: ");    
     scanf("%s",pathtot);    /*j=cptcoveff;*/
   }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   else{    
     strcpy(pathtot,argv[1]);    first=1;
   }    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      /*for(i1=1; i1<=ncodemax[k1];i1++){
   /*cygwin_split_path(pathtot,path,optionfile);        j1++;*/
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        
   /* cutv(path,optionfile,pathtot,'\\');*/        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            prop[i][m]=0.0;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);       
   chdir(path);        for (i=1; i<=imx; i++) { /* Each individual */
   replace(pathc,path);          bool=1;
           if  (cptcovn>0) {
 /*-------- arguments in the command line --------*/            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   /* Log file */                bool=0;
   strcat(filelog, optionfilefiname);          } 
   strcat(filelog,".log");    /* */          if (bool==1) { 
   if((ficlog=fopen(filelog,"w"))==NULL)    {            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     printf("Problem with logfile %s\n",filelog);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     goto end;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficlog,"Log filename:%s\n",filelog);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   fprintf(ficlog,"\n%s",version);                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(ficlog,"\nEnter the parameter file name: ");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                  /*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]]);*/
   fflush(ficlog);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
   /* */                } 
   strcpy(fileres,"r");              }
   strcat(fileres, optionfilefiname);            } /* end selection of waves */
   strcat(fileres,".txt");    /* Other files have txt extension */          }
         }
   /*---------arguments file --------*/        for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            posprop += prop[jk][i]; 
     printf("Problem with optionfile %s\n",optionfile);          } 
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);          
     goto end;          for(jk=1; jk <=nlstate ; jk++){     
   }            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
   strcpy(filereso,"o");                probs[i][jk][j1]= prop[jk][i]/posprop;
   strcat(filereso,fileres);              } else{
   if((ficparo=fopen(filereso,"w"))==NULL) {                if(first==1){
     printf("Problem with Output resultfile: %s\n", filereso);                  first=0;
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);                  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]);
     goto end;                }
   }              }
             } 
   /* Reads comments: lines beginning with '#' */          }/* end jk */ 
   while((c=getc(ficpar))=='#' && c!= EOF){        }/* end i */ 
     ungetc(c,ficpar);      /*} *//* end i1 */
     fgets(line, MAXLINE, ficpar);    } /* end j1 */
     puts(line);    
     fputs(line,ficparo);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   }    /*free_vector(pp,1,nlstate);*/
   ungetc(c,ficpar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   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);  
   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);  /************* Waves Concatenation ***************/
   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);  
 while((c=getc(ficpar))=='#' && c!= EOF){  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)
     ungetc(c,ficpar);  {
     fgets(line, MAXLINE, ficpar);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     puts(line);       Death is a valid wave (if date is known).
     fputs(line,ficparo);       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]
   ungetc(c,ficpar);       and mw[mi+1][i]. dh depends on stepm.
         */
      
   covar=matrix(0,NCOVMAX,1,n);    int i, mi, m;
   cptcovn=0;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;       double sum=0., jmean=0.;*/
     int first;
   ncovmodel=2+cptcovn;    int j, k=0,jk, ju, jl;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    double sum=0.;
      first=0;
   /* Read guess parameters */    jmin=100000;
   /* Reads comments: lines beginning with '#' */    jmax=-1;
   while((c=getc(ficpar))=='#' && c!= EOF){    jmean=0.;
     ungetc(c,ficpar);    for(i=1; i<=imx; i++){
     fgets(line, MAXLINE, ficpar);      mi=0;
     puts(line);      m=firstpass;
     fputs(line,ficparo);      while(s[m][i] <= nlstate){
   }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   ungetc(c,ficpar);          mw[++mi][i]=m;
          if(m >=lastpass)
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          break;
     for(i=1; i <=nlstate; i++)        else
     for(j=1; j <=nlstate+ndeath-1; j++){          m++;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      }/* end while */
       fprintf(ficparo,"%1d%1d",i1,j1);      if (s[m][i] > nlstate){
       if(mle==1)        mi++;     /* Death is another wave */
         printf("%1d%1d",i,j);        /* if(mi==0)  never been interviewed correctly before death */
       fprintf(ficlog,"%1d%1d",i,j);           /* Only death is a correct wave */
       for(k=1; k<=ncovmodel;k++){        mw[mi][i]=m;
         fscanf(ficpar," %lf",&param[i][j][k]);      }
         if(mle==1){  
           printf(" %lf",param[i][j][k]);      wav[i]=mi;
           fprintf(ficlog," %lf",param[i][j][k]);      if(mi==0){
         }        nbwarn++;
         else        if(first==0){
           fprintf(ficlog," %lf",param[i][j][k]);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         fprintf(ficparo," %lf",param[i][j][k]);          first=1;
       }        }
       fscanf(ficpar,"\n");        if(first==1){
       if(mle==1)          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         printf("\n");        }
       fprintf(ficlog,"\n");      } /* end mi==0 */
       fprintf(ficparo,"\n");    } /* End individuals */
     }  
      for(i=1; i<=imx; i++){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
   p=param[1][1];          dh[mi][i]=1;
          else{
   /* Reads comments: lines beginning with '#' */          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   while((c=getc(ficpar))=='#' && c!= EOF){            if (agedc[i] < 2*AGESUP) {
     ungetc(c,ficpar);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     fgets(line, MAXLINE, ficpar);              if(j==0) j=1;  /* Survives at least one month after exam */
     puts(line);              else if(j<0){
     fputs(line,ficparo);                nberr++;
   }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   ungetc(c,ficpar);                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);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                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]);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                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);
   for(i=1; i <=nlstate; i++){              }
     for(j=1; j <=nlstate+ndeath-1; j++){              k=k+1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);              if (j >= jmax){
       printf("%1d%1d",i,j);                jmax=j;
       fprintf(ficparo,"%1d%1d",i1,j1);                ijmax=i;
       for(k=1; k<=ncovmodel;k++){              }
         fscanf(ficpar,"%le",&delti3[i][j][k]);              if (j <= jmin){
         printf(" %le",delti3[i][j][k]);                jmin=j;
         fprintf(ficparo," %le",delti3[i][j][k]);                ijmin=i;
       }              }
       fscanf(ficpar,"\n");              sum=sum+j;
       printf("\n");              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       fprintf(ficparo,"\n");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     }            }
   }          }
   delti=delti3[1][1];          else{
              j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /* Reads comments: lines beginning with '#' */  /*        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]); */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);            k=k+1;
     fgets(line, MAXLINE, ficpar);            if (j >= jmax) {
     puts(line);              jmax=j;
     fputs(line,ficparo);              ijmax=i;
   }            }
   ungetc(c,ficpar);            else if (j <= jmin){
                jmin=j;
   matcov=matrix(1,npar,1,npar);              ijmin=i;
   for(i=1; i <=npar; i++){            }
     fscanf(ficpar,"%s",&str);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     if(mle==1)            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       printf("%s",str);            if(j<0){
     fprintf(ficlog,"%s",str);              nberr++;
     fprintf(ficparo,"%s",str);              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]);
     for(j=1; j <=i; j++){              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]);
       fscanf(ficpar," %le",&matcov[i][j]);            }
       if(mle==1){            sum=sum+j;
         printf(" %.5le",matcov[i][j]);          }
         fprintf(ficlog," %.5le",matcov[i][j]);          jk= j/stepm;
       }          jl= j -jk*stepm;
       else          ju= j -(jk+1)*stepm;
         fprintf(ficlog," %.5le",matcov[i][j]);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       fprintf(ficparo," %.5le",matcov[i][j]);            if(jl==0){
     }              dh[mi][i]=jk;
     fscanf(ficpar,"\n");              bh[mi][i]=0;
     if(mle==1)            }else{ /* We want a negative bias in order to only have interpolation ie
       printf("\n");                    * to avoid the price of an extra matrix product in likelihood */
     fprintf(ficlog,"\n");              dh[mi][i]=jk+1;
     fprintf(ficparo,"\n");              bh[mi][i]=ju;
   }            }
   for(i=1; i <=npar; i++)          }else{
     for(j=i+1;j<=npar;j++)            if(jl <= -ju){
       matcov[i][j]=matcov[j][i];              dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
   if(mle==1)                                   * is higher than the multiple of stepm and negative otherwise.
     printf("\n");                                   */
   fprintf(ficlog,"\n");            }
             else{
               dh[mi][i]=jk+1;
     /*-------- Rewriting paramater file ----------*/              bh[mi][i]=ju;
      strcpy(rfileres,"r");    /* "Rparameterfile */            }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            if(dh[mi][i]==0){
      strcat(rfileres,".");    /* */              dh[mi][i]=1; /* At least one step */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              bh[mi][i]=ju; /* At least one step */
     if((ficres =fopen(rfileres,"w"))==NULL) {              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            }
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;          } /* end if mle */
     }        }
     fprintf(ficres,"#%s\n",version);      } /* end wave */
        }
     /*-------- data file ----------*/    jmean=sum/k;
     if((fic=fopen(datafile,"r"))==NULL)    {    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);
       printf("Problem with datafile: %s\n", datafile);goto end;    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);
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;   }
     }  
   /*********** Tricode ****************************/
     n= lastobs;  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
     severity = vector(1,maxwav);  {
     outcome=imatrix(1,maxwav+1,1,n);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     num=ivector(1,n);    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     moisnais=vector(1,n);     * Boring subroutine which should only output nbcode[Tvar[j]][k]
     annais=vector(1,n);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     moisdc=vector(1,n);     * nbcode[Tvar[j]][1]= 
     andc=vector(1,n);    */
     agedc=vector(1,n);  
     cod=ivector(1,n);    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     weight=vector(1,n);    int modmaxcovj=0; /* Modality max of covariates j */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    int cptcode=0; /* Modality max of covariates j */
     mint=matrix(1,maxwav,1,n);    int modmincovj=0; /* Modality min of covariates j */
     anint=matrix(1,maxwav,1,n);  
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);        cptcoveff=0; 
     tab=ivector(1,NCOVMAX);   
     ncodemax=ivector(1,8);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
     i=1;    /* Loop on covariates without age and products */
     while (fgets(line, MAXLINE, fic) != NULL)    {    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
       if ((i >= firstobs) && (i <=lastobs)) {      for (k=-1; k < maxncov; k++) Ndum[k]=0;
              for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
         for (j=maxwav;j>=1;j--){                                 modality of this covariate Vj*/ 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
           strcpy(line,stra);                                      * If product of Vn*Vm, still boolean *:
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
         }        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                                modality of the nth covariate of individual i. */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        if (ij > modmaxcovj)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          modmaxcovj=ij; 
         else if (ij < modmincovj) 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          modmincovj=ij; 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        if ((ij < -1) && (ij > NCOVMAX)){
           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          exit(1);
         for (j=ncovcol;j>=1;j--){        }else
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         }        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
         num[i]=atol(stra);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                /* getting the maximum value of the modality of the covariate
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
           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;}*/           female is 1, then modmaxcovj=1.*/
       } /* end for loop on individuals i */
         i=i+1;      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       }      fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     }      cptcode=modmaxcovj;
     /* printf("ii=%d", ij);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
        scanf("%d",i);*/     /*for (i=0; i<=cptcode; i++) {*/
   imx=i-1; /* Number of individuals */      for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
   /* for (i=1; i<=imx; i++){        fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          if( k != -1){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
     }*/                               covariate for which somebody answered excluding 
    /*  for (i=1; i<=imx; i++){                               undefined. Usually 2: 0 and 1. */
      if (s[4][i]==9)  s[4][i]=-1;          }
      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]));}*/          ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
                                 covariate for which somebody answered including 
                                 undefined. Usually 3: -1, 0 and 1. */
   /* Calculation of the number of parameter from char model*/        }
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
   Tprod=ivector(1,15);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
   Tvaraff=ivector(1,15);      } /* Ndum[-1] number of undefined modalities */
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);            /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
          /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
   if (strlen(model) >1){         If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
     j=0, j1=0, k1=1, k2=1;         modmincovj=3; modmaxcovj = 7;
     j=nbocc(model,'+');         There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
     j1=nbocc(model,'*');         which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
     cptcovn=j+1;         defining two dummy variables: variables V1_1 and V1_2.
     cptcovprod=j1;         nbcode[Tvar[j]][ij]=k;
             nbcode[Tvar[j]][1]=0;
     strcpy(modelsav,model);         nbcode[Tvar[j]][2]=1;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){         nbcode[Tvar[j]][3]=2;
       printf("Error. Non available option model=%s ",model);      */
       fprintf(ficlog,"Error. Non available option model=%s ",model);      ij=0; /* ij is similar to i but can jumps over null modalities */
       goto end;      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/
     }          if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */
                break;
     for(i=(j+1); i>=1;i--){          }
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */          ij++;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */          nbcode[Tvar[j]][ij]=i;  /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          cptcode = ij; /* New max modality for covar j */
       /*scanf("%d",i);*/      } /* end of loop on modality i=-1 to 1 or more */
       if (strchr(strb,'*')) {  /* Model includes a product */        
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
         if (strcmp(strc,"age")==0) { /* Vn*age */      /*  /\*recode from 0 *\/ */
           cptcovprod--;      /*                               k is a modality. If we have model=V1+V1*sex  */
           cutv(strb,stre,strd,'V');      /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/      /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
           cptcovage++;      /*  } */
             Tage[cptcovage]=i;      /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
             /*printf("stre=%s ", stre);*/      /*  if (ij > ncodemax[j]) { */
         }      /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
         else if (strcmp(strd,"age")==0) { /* or age*Vn */      /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
           cptcovprod--;      /*    break; */
           cutv(strb,stre,strc,'V');      /*  } */
           Tvar[i]=atoi(stre);      /*   }  /\* end of loop on modality k *\/ */
           cptcovage++;    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
           Tage[cptcovage]=i;    
         }   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
         else {  /* Age is not in the model */    
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
           Tvar[i]=ncovcol+k1;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
           Tprod[k1]=i;     Ndum[ij]++; /* Might be supersed V1 + V1*age */
           Tvard[k1][1]=atoi(strc); /* m*/   } 
           Tvard[k1][2]=atoi(stre); /* n */  
           Tvar[cptcovn+k2]=Tvard[k1][1];   ij=0;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
           for (k=1; k<=lastobs;k++)     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];     if((Ndum[i]!=0) && (i<=ncovcol)){
           k1++;       ij++;
           k2=k2+2;       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
         }       Tvaraff[ij]=i; /*For printing (unclear) */
       }     }else{
       else { /* no more sum */         /* Tvaraff[ij]=0; */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/     }
        /*  scanf("%d",i);*/   }
       cutv(strd,strc,strb,'V');   /* ij--; */
       Tvar[i]=atoi(strc);   cptcoveff=ij; /*Number of total covariates*/
       }  
       strcpy(modelsav,stra);    }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/  
     } /* end of loop + */  /*********** Health Expectancies ****************/
   } /* end model */  
    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("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);    /* Health expectancies, no variances */
   scanf("%d ",i);*/    int i, j, nhstepm, hstepm, h, nstepm;
     fclose(fic);    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     /*  if(mle==1){*/    double ***p3mat;
     if (weightopt != 1) { /* Maximisation without weights*/    double eip;
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }    pstamp(ficreseij);
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     agev=matrix(1,maxwav,1,imx);    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
     for (i=1; i<=imx; i++) {      for(j=1; j<=nlstate;j++){
       for(m=2; (m<= maxwav); m++) {        fprintf(ficreseij," e%1d%1d ",i,j);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      }
          anint[m][i]=9999;      fprintf(ficreseij," e%1d. ",i);
          s[m][i]=-1;    }
        }    fprintf(ficreseij,"\n");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }    
     }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     for (i=1; i<=imx; i++)  {    }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    else  hstepm=estepm;   
       for(m=1; (m<= maxwav); m++){    /* We compute the life expectancy from trapezoids spaced every estepm months
         if(s[m][i] >0){     * This is mainly to measure the difference between two models: for example
           if (s[m][i] >= nlstate+1) {     * if stepm=24 months pijx are given only every 2 years and by summing them
             if(agedc[i]>0)     * we are calculating an estimate of the Life Expectancy assuming a linear 
               if(moisdc[i]!=99 && andc[i]!=9999)     * progression in between and thus overestimating or underestimating according
                 agev[m][i]=agedc[i];     * to the curvature of the survival function. If, for the same date, we 
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/     * estimate the model with stepm=1 month, we can keep estepm to 24 months
            else {     * to compare the new estimate of Life expectancy with the same linear 
               if (andc[i]!=9999){     * hypothesis. A more precise result, taking into account a more precise
               printf("Warning negative age at death: %d line:%d\n",num[i],i);     * curvature will be obtained if estepm is as small as stepm. */
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    /* 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. 
           else if(s[m][i] !=9){ /* Should no more exist */       Look at hpijx to understand the reason of that which relies in memory size
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);       and note for a fixed period like estepm months */
             if(mint[m][i]==99 || anint[m][i]==9999)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               agev[m][i]=1;       survival function given by stepm (the optimization length). Unfortunately it
             else if(agev[m][i] <agemin){       means that if the survival funtion is printed only each two years of age and if
               agemin=agev[m][i];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       results. So we changed our mind and took the option of the best precision.
             }    */
             else if(agev[m][i] >agemax){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    agelim=AGESUP;
             }    /* If stepm=6 months */
             /*agev[m][i]=anint[m][i]-annais[i];*/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             /*   agev[m][i] = age[i]+2*m;*/         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           }      
           else { /* =9 */  /* nhstepm age range expressed in number of stepm */
             agev[m][i]=1;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
             s[m][i]=-1;    /* 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 */
         else /*= 0 Unknown */    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           agev[m][i]=1;  
       }    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 */ 
     for (i=1; i<=imx; i++)  {      /* if (stepm >= YEARM) hstepm=1;*/
       for(m=1; (m<= maxwav); m++){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         if (s[m][i] > (nlstate+ndeath)) {  
           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);        /* If stepm=6 months */
           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);        /* Computed by stepm unit matrices, product of hstepma matrices, stored
           goto end;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
         }      
       }      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     }      
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 printf("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);      printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     free_vector(severity,1,maxwav);      
     free_imatrix(outcome,1,maxwav+1,1,n);      /* Computing expectancies */
     free_vector(moisnais,1,n);      for(i=1; i<=nlstate;i++)
     free_vector(annais,1,n);        for(j=1; j<=nlstate;j++)
     /* free_matrix(mint,1,maxwav,1,n);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        free_matrix(anint,1,maxwav,1,n);*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     free_vector(moisdc,1,n);            
     free_vector(andc,1,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]);*/
   
              }
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      fprintf(ficreseij,"%3.0f",age );
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      for(i=1; i<=nlstate;i++){
            eip=0;
     /* Concatenates waves */        for(j=1; j<=nlstate;j++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
       Tcode=ivector(1,100);        fprintf(ficreseij,"%9.4f", eip );
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      }
       ncodemax[1]=1;      fprintf(ficreseij,"\n");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      
          }
    codtab=imatrix(1,100,1,10);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    h=0;    printf("\n");
    m=pow(2,cptcoveff);    fprintf(ficlog,"\n");
      
    for(k=1;k<=cptcoveff; k++){  }
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){  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[] )
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  
            h++;  {
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    /* Covariances of health expectancies eij and of total life expectancies according
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/     to initial status i, ei. .
          }    */
        }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      }    int nhstepma, nstepma; /* Decreasing with age */
    }    double age, agelim, hf;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    double ***p3matp, ***p3matm, ***varhe;
       codtab[1][2]=1;codtab[2][2]=2; */    double **dnewm,**doldm;
    /* for(i=1; i <=m ;i++){    double *xp, *xm;
       for(k=1; k <=cptcovn; k++){    double **gp, **gm;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    double ***gradg, ***trgradg;
       }    int theta;
       printf("\n");  
       }    double eip, vip;
       scanf("%d",i);*/  
        varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
    /* Calculates basic frequencies. Computes observed prevalence at single age    xp=vector(1,npar);
        and prints on file fileres'p'. */    xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
        doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
        
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficresstdeij);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresstdeij,"# Age");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for(i=1; i<=nlstate;i++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      for(j=1; j<=nlstate;j++)
              fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     /* For Powell, parameters are in a vector p[] starting at p[1]      fprintf(ficresstdeij," e%1d. ",i);
        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) */    fprintf(ficresstdeij,"\n");
   
     if(mle==1){    pstamp(ficrescveij);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     }    fprintf(ficrescveij,"# Age");
        for(i=1; i<=nlstate;i++)
     /*--------- results files --------------*/      for(j=1; j<=nlstate;j++){
     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);        cptj= (j-1)*nlstate+i;
          for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
    jk=1;            cptj2= (j2-1)*nlstate+i2;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            if(cptj2 <= cptj)
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
    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++){    fprintf(ficrescveij,"\n");
        if (k != i)    
          {    if(estepm < stepm){
            printf("%d%d ",i,k);      printf ("Problem %d lower than %d\n",estepm, stepm);
            fprintf(ficlog,"%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);    else  hstepm=estepm;   
            for(j=1; j <=ncovmodel; j++){    /* We compute the life expectancy from trapezoids spaced every estepm months
              printf("%f ",p[jk]);     * This is mainly to measure the difference between two models: for example
              fprintf(ficlog,"%f ",p[jk]);     * if stepm=24 months pijx are given only every 2 years and by summing them
              fprintf(ficres,"%f ",p[jk]);     * we are calculating an estimate of the Life Expectancy assuming a linear 
              jk++;     * progression in between and thus overestimating or underestimating according
            }     * to the curvature of the survival function. If, for the same date, we 
            printf("\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
            fprintf(ficlog,"\n");     * to compare the new estimate of Life expectancy with the same linear 
            fprintf(ficres,"\n");     * 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 */
    if(mle==1){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      /* Computing hessian and covariance matrix */       nhstepm is the number of hstepm from age to agelim 
      ftolhess=ftol; /* Usually correct */       nstepm is the number of stepm from age to agelin. 
      hesscov(matcov, p, npar, delti, ftolhess, func);       Look at hpijx to understand the reason of that which relies in memory size
    }       and note for a fixed period like estepm months */
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
    printf("# Scales (for hessian or gradient estimation)\n");       survival function given by stepm (the optimization length). Unfortunately it
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");       means that if the survival funtion is printed only each two years of age and if
    for(i=1,jk=1; i <=nlstate; i++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      for(j=1; j <=nlstate+ndeath; j++){       results. So we changed our mind and took the option of the best precision.
        if (j!=i) {    */
          fprintf(ficres,"%1d%1d",i,j);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
          printf("%1d%1d",i,j);  
          fprintf(ficlog,"%1d%1d",i,j);    /* If stepm=6 months */
          for(k=1; k<=ncovmodel;k++){    /* nhstepm age range expressed in number of stepm */
            printf(" %.5e",delti[jk]);    agelim=AGESUP;
            fprintf(ficlog," %.5e",delti[jk]);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
            fprintf(ficres," %.5e",delti[jk]);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
            jk++;    /* if (stepm >= YEARM) hstepm=1;*/
          }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          printf("\n");    
          fprintf(ficlog,"\n");    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          fprintf(ficres,"\n");    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);
    k=1;  
    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");    for (age=bage; age<=fage; age ++){ 
    if(mle==1)      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      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");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    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");      /* if (stepm >= YEARM) hstepm=1;*/
    for(i=1;i<=npar;i++){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
      /*  if (k>nlstate) k=1;  
          i1=(i-1)/(ncovmodel*nlstate)+1;      /* If stepm=6 months */
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          printf("%s%d%d",alph[k],i1,tab[i]);*/         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      fprintf(ficres,"%3d",i);      
      if(mle==1)      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        printf("%3d",i);  
      fprintf(ficlog,"%3d",i);      /* Computing  Variances of health expectancies */
      for(j=1; j<=i;j++){      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
        fprintf(ficres," %.5e",matcov[i][j]);         decrease memory allocation */
        if(mle==1)      for(theta=1; theta <=npar; theta++){
          printf(" %.5e",matcov[i][j]);        for(i=1; i<=npar; i++){ 
        fprintf(ficlog," %.5e",matcov[i][j]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
      fprintf(ficres,"\n");        }
      if(mle==1)        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
        printf("\n");        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
      fprintf(ficlog,"\n");    
      k++;        for(j=1; j<= nlstate; j++){
    }          for(i=1; i<=nlstate; i++){
                for(h=0; h<=nhstepm-1; h++){
    while((c=getc(ficpar))=='#' && c!= EOF){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
      ungetc(c,ficpar);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
      fgets(line, MAXLINE, ficpar);            }
      puts(line);          }
      fputs(line,ficparo);        }
    }       
    ungetc(c,ficpar);        for(ij=1; ij<= nlstate*nlstate; ij++)
    estepm=0;          for(h=0; h<=nhstepm-1; h++){
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
    if (estepm==0 || estepm < stepm) estepm=stepm;          }
    if (fage <= 2) {      }/* End theta */
      bage = ageminpar;      
      fage = agemaxpar;      
    }      for(h=0; h<=nhstepm-1; h++)
            for(j=1; j<=nlstate*nlstate;j++)
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          for(theta=1; theta <=npar; theta++)
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            trgradg[h][j][theta]=gradg[h][theta][j];
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      
      
    while((c=getc(ficpar))=='#' && c!= EOF){       for(ij=1;ij<=nlstate*nlstate;ij++)
      ungetc(c,ficpar);        for(ji=1;ji<=nlstate*nlstate;ji++)
      fgets(line, MAXLINE, ficpar);          varhe[ij][ji][(int)age] =0.;
      puts(line);  
      fputs(line,ficparo);       printf("%d|",(int)age);fflush(stdout);
    }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
    ungetc(c,ficpar);       for(h=0;h<=nhstepm-1;h++){
          for(k=0;k<=nhstepm-1;k++){
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for(ij=1;ij<=nlstate*nlstate;ij++)
                for(ji=1;ji<=nlstate*nlstate;ji++)
    while((c=getc(ficpar))=='#' && c!= EOF){              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
      ungetc(c,ficpar);        }
      fgets(line, MAXLINE, ficpar);      }
      puts(line);  
      fputs(line,ficparo);      /* Computing expectancies */
    }      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
    ungetc(c,ficpar);      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++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            
             /* 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]);*/
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
   fprintf(ficparo,"pop_based=%d\n",popbased);            }
   fprintf(ficres,"pop_based=%d\n",popbased);    
        fprintf(ficresstdeij,"%3.0f",age );
   while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1; i<=nlstate;i++){
     ungetc(c,ficpar);        eip=0.;
     fgets(line, MAXLINE, ficpar);        vip=0.;
     puts(line);        for(j=1; j<=nlstate;j++){
     fputs(line,ficparo);          eip += eij[i][j][(int)age];
   }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   ungetc(c,ficpar);            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]) );
   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);        }
 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);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
 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);      }
       fprintf(ficresstdeij,"\n");
   
 while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficrescveij,"%3.0f",age );
     ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);        for(j=1; j<=nlstate;j++){
     puts(line);          cptj= (j-1)*nlstate+i;
     fputs(line,ficparo);          for(i2=1; i2<=nlstate;i2++)
   }            for(j2=1; j2<=nlstate;j2++){
   ungetc(c,ficpar);              cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            }
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }
       fprintf(ficrescveij,"\n");
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);     
     }
 /*------------ gnuplot -------------*/    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   strcpy(optionfilegnuplot,optionfilefiname);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   strcat(optionfilegnuplot,".gp");    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     printf("Problem with file %s",optionfilegnuplot);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficgp);    printf("\n");
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    fprintf(ficlog,"\n");
 /*--------- index.htm --------*/  
     free_vector(xm,1,npar);
   strcpy(optionfilehtm,optionfile);    free_vector(xp,1,npar);
   strcat(optionfilehtm,".htm");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     printf("Problem with %s \n",optionfilehtm), exit(0);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }  }
   
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n  /************ Variance ******************/
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n  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[])
 \n  {
 Total number of observations=%d <br>\n    /* Variance of health expectancies */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 <hr  size=\"2\" color=\"#EC5E5E\">    /* double **newm;*/
  <ul><li><h4>Parameter files</h4>\n    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
  - 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    int movingaverage();
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);    double **dnewm,**doldm;
   fclose(fichtm);    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    int k;
      double *xp;
 /*------------ free_vector  -------------*/    double **gp, **gm;  /* for var eij */
  chdir(path);    double ***gradg, ***trgradg; /*for var eij */
      double **gradgp, **trgradgp; /* for var p point j */
  free_ivector(wav,1,imx);    double *gpp, *gmp; /* for var p point j */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      double ***p3mat;
  free_ivector(num,1,n);    double age,agelim, hf;
  free_vector(agedc,1,n);    double ***mobaverage;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    int theta;
  fclose(ficparo);    char digit[4];
  fclose(ficres);    char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   /*--------------- Prevalence limit --------------*/  
      if(popbased==1){
   strcpy(filerespl,"pl");      if(mobilav!=0)
   strcat(filerespl,fileres);        strcpy(digitp,"-populbased-mobilav-");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      else strcpy(digitp,"-populbased-nomobil-");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    }
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;    else 
   }      strcpy(digitp,"-stablbased-");
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    if (mobilav!=0) {
   fprintf(ficrespl,"#Prevalence limit\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficrespl,"#Age ");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   fprintf(ficrespl,"\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        }
   prlim=matrix(1,nlstate,1,nlstate);    }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcpy(fileresprobmorprev,"prmorprev"); 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    sprintf(digit,"%-d",ij);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   k=0;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   agebase=ageminpar;    strcat(fileresprobmorprev,fileres);
   agelim=agemaxpar;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   ftolpl=1.e-10;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   i1=cptcoveff;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   if (cptcovn < 1){i1=1;}    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   for(cptcov=1;cptcov<=i1;cptcov++){   
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         k=k+1;    pstamp(ficresprobmorprev);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    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(ficrespl,"\n#******");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         printf("\n#******");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficlog,"\n#******");      fprintf(ficresprobmorprev," p.%-d SE",j);
         for(j=1;j<=cptcoveff;j++) {      for(i=1; i<=nlstate;i++)
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,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(ficresprobmorprev,"\n");
         }    fprintf(ficgp,"\n# Routine varevsij");
         fprintf(ficrespl,"******\n");    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
         printf("******\n");    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(ficlog,"******\n");    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
          /*   } */
         for (age=agebase; age<=agelim; age++){    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    pstamp(ficresvij);
           fprintf(ficrespl,"%.0f",age );    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
           for(i=1; i<=nlstate;i++)    if(popbased==1)
           fprintf(ficrespl," %.5f", prlim[i][i]);      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);
           fprintf(ficrespl,"\n");    else
         }      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
       }    fprintf(ficresvij,"# Age");
     }    for(i=1; i<=nlstate;i++)
   fclose(ficrespl);      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   /*------------- h Pij x at various ages ------------*/    fprintf(ficresvij,"\n");
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    xp=vector(1,npar);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    dnewm=matrix(1,nlstate,1,npar);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    doldm=matrix(1,nlstate,1,nlstate);
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("Computing pij: result on file '%s' \n", filerespij);  
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    gmp=vector(nlstate+1,nlstate+ndeath);
   /*if (stepm<=24) stepsize=2;*/    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   agelim=AGESUP;    if(estepm < stepm){
   hstepm=stepsize*YEARM; /* Every year of age */      printf ("Problem %d lower than %d\n",estepm, stepm);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    }
     else  hstepm=estepm;   
   /* hstepm=1;   aff par mois*/    /* 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. 
   k=0;       nhstepm is the number of hstepm from age to agelim 
   for(cptcov=1;cptcov<=i1;cptcov++){       nstepm is the number of stepm from age to agelin. 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       Look at function hpijx to understand why (it is linked to memory size questions) */
       k=k+1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficrespij,"\n#****** ");       survival function given by stepm (the optimization length). Unfortunately it
         for(j=1;j<=cptcoveff;j++)       means that if the survival funtion is printed every two years of age and if
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficrespij,"******\n");       results. So we changed our mind and took the option of the best precision.
            */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    agelim = AGESUP;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    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=nhstepm*YEARM; aff par mois*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           oldm=oldms;savm=savms;      gp=matrix(0,nhstepm,1,nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        gm=matrix(0,nhstepm,1,nlstate);
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)      for(theta=1; theta <=npar; theta++){
               fprintf(ficrespij," %1d-%1d",i,j);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           fprintf(ficrespij,"\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            for (h=0; h<=nhstepm; h++){        }
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             for(i=1; i<=nlstate;i++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        if (popbased==1) {
             fprintf(ficrespij,"\n");          if(mobilav ==0){
              }            for(i=1; i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              prlim[i][i]=probs[(int)age][i][ij];
           fprintf(ficrespij,"\n");          }else{ /* mobilav */ 
         }            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
         }
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    
         for(j=1; j<= nlstate; j++){
   fclose(ficrespij);          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];
   /*---------- Forecasting ------------------*/          }
   if((stepm == 1) && (strcmp(model,".")==0)){        }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        /* This for computing probability of death (h=1 means
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   else{        */
     erreur=108;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     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);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     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);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   }        }    
          /* end probability of death */
   
   /*---------- Health expectancies and variances ------------*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   strcpy(filerest,"t");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   strcat(filerest,fileres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if((ficrest=fopen(filerest,"w"))==NULL) {   
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        if (popbased==1) {
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
   printf("Computing Total LEs with variances: file '%s' \n", filerest);              prlim[i][i]=probs[(int)age][i][ij];
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   strcpy(filerese,"e");          }
   strcat(filerese,fileres);        }
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);          }
         }
   strcpy(fileresv,"v");        /* This for computing probability of death (h=1 means
   strcat(fileresv,fileres);           computed over hstepm matrices product = hstepm*stepm months) 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {           as a weighted average of prlim.
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        */
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        }    
   calagedate=-1;        /* end probability of death */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
         for(j=1; j<= nlstate; j++) /* vareij */
   k=0;          for(h=0; h<=nhstepm; h++){
   for(cptcov=1;cptcov<=i1;cptcov++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          }
       k=k+1;  
       fprintf(ficrest,"\n#****** ");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       for(j=1;j<=cptcoveff;j++)          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
       fprintf(ficrest,"******\n");  
       } /* End theta */
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
       fprintf(ficresvij,"\n#****** ");          for(theta=1; theta <=npar; theta++)
       for(j=1;j<=cptcoveff;j++)            trgradg[h][j][theta]=gradg[h][theta][j];
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvij,"******\n");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          trgradgp[j][theta]=gradgp[theta][j];
       oldm=oldms;savm=savms;    
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for(i=1;i<=nlstate;i++)
       oldm=oldms;savm=savms;        for(j=1;j<=nlstate;j++)
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);          vareij[i][j][(int)age] =0.;
       if(popbased==1){  
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);      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]);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          for(i=1;i<=nlstate;i++)
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            for(j=1;j<=nlstate;j++)
       fprintf(ficrest,"\n");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       epj=vector(1,nlstate+1);      }
       for(age=bage; age <=fage ;age++){    
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      /* pptj */
         if (popbased==1) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           for(i=1; i<=nlstate;i++)      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
             prlim[i][i]=probs[(int)age][i][k];      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
                  varppt[j][i]=doldmp[j][i];
         fprintf(ficrest," %4.0f",age);      /* end ppptj */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      /*  x centered again */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/   
           }      if (popbased==1) {
           epj[nlstate+1] +=epj[j];        if(mobilav ==0){
         }          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         for(i=1, vepp=0.;i <=nlstate;i++)        }else{ /* mobilav */ 
           for(j=1;j <=nlstate;j++)          for(i=1; i<=nlstate;i++)
             vepp += vareij[i][j][(int)age];            prlim[i][i]=mobaverage[(int)age][i][ij];
         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]));               
         }      /* This for computing probability of death (h=1 means
         fprintf(ficrest,"\n");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       }         as a weighted average of prlim.
     }      */
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
 free_matrix(mint,1,maxwav,1,n);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     free_vector(weight,1,n);      }    
   fclose(ficreseij);      /* end probability of death */
   fclose(ficresvij);  
   fclose(ficrest);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   fclose(ficpar);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   free_vector(epj,1,nlstate+1);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
   /*------- Variance limit prevalence------*/            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
   strcpy(fileresvpl,"vpl");      } 
   strcat(fileresvpl,fileres);      fprintf(ficresprobmorprev,"\n");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      fprintf(ficresvij,"%.0f ",age );
     exit(0);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
   k=0;      fprintf(ficresvij,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){      free_matrix(gp,0,nhstepm,1,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      free_matrix(gm,0,nhstepm,1,nlstate);
       k=k+1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fprintf(ficresvpl,"\n#****** ");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       for(j=1;j<=cptcoveff;j++)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    } /* End age */
       fprintf(ficresvpl,"******\n");    free_vector(gpp,nlstate+1,nlstate+ndeath);
          free_vector(gmp,nlstate+1,nlstate+ndeath);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       oldm=oldms;savm=savms;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    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); */
   fclose(ficresvpl);  /*   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); */
   /*---------- End : free ----------------*/    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    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));
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    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);
    */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,nlstate);
   free_matrix(matcov,1,npar,1,npar);    free_matrix(dnewm,1,nlstate,1,npar);
   free_vector(delti,1,npar);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(agev,1,maxwav,1,imx);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(fichtm,"\n</body>");    fclose(ficresprobmorprev);
   fclose(fichtm);    fflush(ficgp);
   fclose(ficgp);    fflush(fichtm); 
    }  /* end varevsij */
   
   if(erreur >0){  /************ Variance of prevlim ******************/
     printf("End of Imach with error or warning %d\n",erreur);  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[])
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);  {
   }else{    /* Variance of prevalence limit */
    printf("End of Imach\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
    fprintf(ficlog,"End of Imach\n");  
   }    double **dnewm,**doldm;
   printf("See log file on %s\n",filelog);    int i, j, nhstepm, hstepm;
   fclose(ficlog);    double *xp;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    double *gp, *gm;
      double **gradg, **trgradg;
   /* 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 age,agelim;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    int theta;
   /*------ End -----------*/    
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
  end:    fprintf(ficresvpl,"# Age");
 #ifdef windows    for(i=1; i<=nlstate;i++)
   /* chdir(pathcd);*/        fprintf(ficresvpl," %1d-%1d",i,i);
 #endif    fprintf(ficresvpl,"\n");
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    xp=vector(1,npar);
  /*system("cd ../gp37mgw");*/    dnewm=matrix(1,nlstate,1,npar);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    doldm=matrix(1,nlstate,1,nlstate);
  strcpy(plotcmd,GNUPLOTPROGRAM);    
  strcat(plotcmd," ");    hstepm=1*YEARM; /* Every year of age */
  strcat(plotcmd,optionfilegnuplot);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
  system(plotcmd);    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 #ifdef windows      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   while (z[0] != 'q') {      if (stepm >= YEARM) hstepm=1;
     /* chdir(path); */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      gradg=matrix(1,npar,1,nlstate);
     scanf("%s",z);      gp=vector(1,nlstate);
     if (z[0] == 'c') system("./imach");      gm=vector(1,nlstate);
     else if (z[0] == 'e') system(optionfilehtm);  
     else if (z[0] == 'g') system(plotcmd);      for(theta=1; theta <=npar; theta++){
     else if (z[0] == 'q') exit(0);        for(i=1; i<=npar; i++){ /* Computes gradient */
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #endif        }
 }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           if(nagesqr==1)
             cov[3]= age*age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
            printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
          }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      /* } /\* end i1 *\/ */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      /* } /\* end i1 *\/ */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
     for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficgp,"# initial state %d\n",i);
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           fprintf(ficgp,"#   current state %d\n",k);
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
             jk++; 
           }
           fprintf(ficgp,"\n");
         }
       }
      }
     fprintf(ficgp,"##############\n#\n");
   
     /*goto avoid;*/
     fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
     fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
     fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
     fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
     fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
     fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
     fprintf(ficgp,"#\n");
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        fprintf(ficgp,"# ng=%d\n",ng);
        fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"#    jk=%d\n",jk);
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  if(nagesqr==0)
                    fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                else
                  if(nagesqr==0)
                    fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel-nagesqr; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){ 
                  if(nagesqr==0)
                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
     
                  ij=1;
                  for(j=3; j <=ncovmodel-nagesqr; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
      * - nagesqr = 1 if age*age in the model, otherwise 0.
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
      * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
     char *strpt;
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       strcpy(modelsav,model); 
       if ((strpt=strstr(model,"age*age")) !=0){
         printf(" strpt=%s, model=%s\n",strpt, model);
         if(strpt != model){
         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
    corresponding column of parameters.\n",model);
         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
    corresponding column of parameters.\n",model); fflush(ficlog);
         return 1;
       }
   
         nagesqr=1;
         if (strstr(model,"+age*age") !=0)
           substrchaine(modelsav, model, "+age*age");
         else if (strstr(model,"age*age+") !=0)
           substrchaine(modelsav, model, "age*age+");
         else 
           substrchaine(modelsav, model, "age*age");
       }else
         nagesqr=0;
       if (strlen(modelsav) >1){
         j=nbocc(modelsav,'+'); /**< j=Number of '+' */
         j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
         cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
         cptcovt= j+1; /* Number of total covariates in the model, not including
                      * cst, age and age*age 
                      * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated 
                     * separately: ncovn=4- 2=2 (V1+V3). */
         cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
         cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
   
       
         /*   Design
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
          *  <          ncovcol=8                >
          * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
          *   k=  1    2      3       4     5       6      7        8
          *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
          *  covar[k,i], value of kth covariate if not including age for individual i:
          *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
          *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
          *  Tage[++cptcovage]=k
          *       if products, new covar are created after ncovcol with k1
          *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
          *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
          *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
          *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
          *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
          *  <          ncovcol=8                >
          *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
          *          k=  1    2      3       4     5       6      7        8    9   10   11  12
          *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
          * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          * p Tprod[1]@2={                         6, 5}
          *p Tvard[1][1]@4= {7, 8, 5, 6}
          * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
          *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          *How to reorganize?
          * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
          * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          *       {2,   1,     4,      8,    5,      6,     3,       7}
          * Struct []
          */
   
         /* This loop fills the array Tvar from the string 'model'.*/
         /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
         /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
         /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
         /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
         /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
         /*        k=1 Tvar[1]=2 (from V2) */
         /*        k=5 Tvar[5] */
         /* for (k=1; k<=cptcovn;k++) { */
         /*        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
         /*        } */
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
         /*
          * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
         for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
         cptcovage=0;
         for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                            modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
           if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
           /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
           /*scanf("%d",i);*/
           if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
             cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
             if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
               /* covar is not filled and then is empty */
               cptcovprod--;
               cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
               Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
               cptcovage++; /* Sums the number of covariates which include age as a product */
               Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
               /*printf("stre=%s ", stre);*/
             } else if (strcmp(strd,"age")==0) { /* or age*Vn */
               cptcovprod--;
               cutl(stre,strb,strc,'V');
               Tvar[k]=atoi(stre);
               cptcovage++;
               Tage[cptcovage]=k;
             } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
               /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
               cptcovn++;
               cptcovprodnoage++;k1++;
               cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
               Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                      because this model-covariate is a construction we invent a new column
                                      ncovcol + k1
                                      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                      Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
               cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
               Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
               Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
               Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
               k2=k2+2;
               Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
               Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
               for (i=1; i<=lastobs;i++){
                 /* Computes the new covariate which is a product of
                    covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                 covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
               }
             } /* End age is not in the model */
           } /* End if model includes a product */
           else { /* no more sum */
             /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
             /*  scanf("%d",i);*/
             cutl(strd,strc,strb,'V');
             ks++; /**< Number of simple covariates */
             cptcovn++;
             Tvar[k]=atoi(strd);
           }
           strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
           /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
             scanf("%d",i);*/
         } /* end of loop + on total covariates */
       } /* end if strlen(modelsave == 0) age*age might exist */
     } /* end if strlen(model == 0) */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo(int logged)
    {
      /* #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-");
              if(logged) fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for "); if (logged) 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) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");if(logged) fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");if(logged) 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"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); if(logged) 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__);
      if(logged) 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);
            if(logged) 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()); 
      if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              if (logged) fprintf(ficlog, "\nThe 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=0.;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum=0.; /* 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=0;
     int i1, j1, jk, stepsize=0;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm=0, nhstepm=0;
     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=0., agebase=0.;
     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
     syscompilerinfo(0);
     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(0);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /* Main ---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
       model[strlen(model)-1]='\0';
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     /* if(model[0]=='#'|| model[0]== '\0'){ */
     if(model[0]=='#'){
       printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
    'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
    'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
       if(mle != -1){
         printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
         exit(1);
       }
     }
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
     else
       ncovmodel=2; /* Constant and age */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You chose 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 chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You chose 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 */
     ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
   /* Main decodemodel */
   
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] is the maximum value of this jth covariate */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              * For k=4 covariates, h goes from 1 to 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
              *     h\k   1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /* codtab[12][3]=1; */
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /* Initialisation of ----------- gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
   
   
     /* Initialisation of --------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
       /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
       /*     gsl_vector_set(x, 0, 0.0268); */
       /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 mortality only */
     /* Standard maximisation */
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* again, to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%12.7f ",p[jk]);
               fprintf(ficlog,"%12.7f ",p[jk]);
               fprintf(ficres,"%12.7f ",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(ncodemaxwundef,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.1.51  
changed lines
  Added in v.1.192


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