Diff for /imach/src/imach.c between versions 1.50 and 1.184

version 1.50, 2002/06/26 23:25:02 version 1.184, 2015/03/11 11:52:39
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.184  2015/03/11 11:52:39  brouard
      Summary: Back from Windows 8. Intel Compiler
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.183  2015/03/10 20:34:32  brouard
   first survey ("cross") where individuals from different ages are    Summary: 0.98q0, trying with directest, mnbrak fixed
   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    We use directest instead of original Powell test; probably no
   second wave of interviews ("longitudinal") which measure each change    incidence on the results, but better justifications;
   (if any) in individual health status.  Health expectancies are    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   computed from the time spent in each health state according to a    wrong results.
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.182  2015/02/12 08:19:57  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: Trying to keep directest which seems simpler and more general
   probability to be observed in state j at the second wave    Author: Nicolas Brouard
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.181  2015/02/11 23:22:24  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Summary: Comments on Powell added
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Author:
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.180  2015/02/11 17:33:45  brouard
     Summary: Finishing move from main to function (hpijx and prevalence_limit)
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.179  2015/01/04 09:57:06  brouard
   identical for each individual. Also, if a individual missed an    Summary: back to OS/X
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.178  2015/01/04 09:35:48  brouard
     *** empty log message ***
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.177  2015/01/03 18:40:56  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: Still testing ilc32 on OSX
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.176  2015/01/03 16:45:04  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    *** empty log message ***
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.174  2015/01/03 16:15:49  brouard
      Summary: Still in cross-compilation
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.173  2015/01/03 12:06:26  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: trying to detect cross-compilation
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.172  2014/12/27 12:07:47  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.171  2014/12/23 13:26:59  brouard
      Summary: Back from Visual C
 #include <math.h>  
 #include <stdio.h>    Still problem with utsname.h on Windows
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "gnuplot"    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.169  2014/12/22 23:08:31  brouard
 /*#define DEBUG*/    Summary: 0.98p
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.168  2014/12/22 15:17:42  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: update
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.167  2014/12/22 13:50:56  brouard
 #define NINTERVMAX 8    Summary: Testing uname and compiler version and if compiled 32 or 64
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Testing on Linux 64
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.166  2014/12/22 11:40:47  brouard
 #define YEARM 12. /* Number of months per year */    *** empty log message ***
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.165  2014/12/16 11:20:36  brouard
 #ifdef windows    Summary: After compiling on Visual C
 #define DIRSEPARATOR '\\'  
 #define ODIRSEPARATOR '/'    * imach.c (Module): Merging 1.61 to 1.162
 #else  
 #define DIRSEPARATOR '/'    Revision 1.164  2014/12/16 10:52:11  brouard
 #define ODIRSEPARATOR '\\'    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #endif  
     * imach.c (Module): Merging 1.61 to 1.162
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    Revision 1.163  2014/12/16 10:30:11  brouard
 int nvar;    * imach.c (Module): Merging 1.61 to 1.162
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.162  2014/09/25 11:43:39  brouard
 int nlstate=2; /* Number of live states */    Summary: temporary backup 0.99!
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.1  2014/09/16 11:06:58  brouard
 int popbased=0;    Summary: With some code (wrong) for nlopt
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Author:
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.161  2014/09/15 20:41:41  brouard
 int mle, weightopt;    Summary: Problem with macro SQR on Intel compiler
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.160  2014/09/02 09:24:05  brouard
 double jmean; /* Mean space between 2 waves */    *** empty log message ***
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.159  2014/09/01 10:34:10  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Summary: WIN32
 FILE *ficlog;    Author: Brouard
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficresprobmorprev;    Revision 1.158  2014/08/27 17:11:51  brouard
 FILE *fichtm; /* Html File */    *** empty log message ***
 FILE *ficreseij;  
 char filerese[FILENAMELENGTH];    Revision 1.157  2014/08/27 16:26:55  brouard
 FILE  *ficresvij;    Summary: Preparing windows Visual studio version
 char fileresv[FILENAMELENGTH];    Author: Brouard
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    In order to compile on Visual studio, time.h is now correct and time_t
 char title[MAXLINE];    and tm struct should be used. difftime should be used but sometimes I
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    just make the differences in raw time format (time(&now).
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */    Revision 1.156  2014/08/25 20:10:10  brouard
 char filerest[FILENAMELENGTH];    *** empty log message ***
 char fileregp[FILENAMELENGTH];  
 char popfile[FILENAMELENGTH];    Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Author: Brouard
   
 #define NR_END 1    Revision 1.154  2014/06/20 17:32:08  brouard
 #define FREE_ARG char*    Summary: Outputs now all graphs of convergence to period prevalence
 #define FTOL 1.0e-10  
     Revision 1.153  2014/06/20 16:45:46  brouard
 #define NRANSI    Summary: If 3 live state, convergence to period prevalence on same graph
 #define ITMAX 200    Author: Brouard
   
 #define TOL 2.0e-4    Revision 1.152  2014/06/18 17:54:09  brouard
     Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.151  2014/06/18 16:43:30  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    *** empty log message ***
   
 #define GOLD 1.618034    Revision 1.150  2014/06/18 16:42:35  brouard
 #define GLIMIT 100.0    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 #define TINY 1.0e-20    Author: brouard
   
 static double maxarg1,maxarg2;    Revision 1.149  2014/06/18 15:51:14  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Summary: Some fixes in parameter files errors
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Author: Nicolas Brouard
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.148  2014/06/17 17:38:48  brouard
 #define rint(a) floor(a+0.5)    Summary: Nothing new
     Author: Brouard
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Just a new packaging for OS/X version 0.98nS
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.147  2014/06/16 10:33:11  brouard
 int imx;    *** empty log message ***
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.146  2014/06/16 10:20:28  brouard
     Summary: Merge
 int estepm;    Author: Brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Merge, before building revised version.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.145  2014/06/10 21:23:15  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Summary: Debugging with valgrind
 double **pmmij, ***probs, ***mobaverage;    Author: Nicolas Brouard
 double dateintmean=0;  
     Lot of changes in order to output the results with some covariates
 double *weight;    After the Edimburgh REVES conference 2014, it seems mandatory to
 int **s; /* Status */    improve the code.
 double *agedc, **covar, idx;    No more memory valgrind error but a lot has to be done in order to
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    continue the work of splitting the code into subroutines.
     Also, decodemodel has been improved. Tricode is still not
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    optimal. nbcode should be improved. Documentation has been added in
 double ftolhess; /* Tolerance for computing hessian */    the source code.
   
 /**************** split *************************/    Revision 1.143  2014/01/26 09:45:38  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 {  
    char *s;                             /* pointer */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    int  l1, l2;                         /* length counters */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
    l1 = strlen( path );                 /* length of path */    Revision 1.142  2014/01/26 03:57:36  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    Revision 1.141  2014/01/26 02:42:01  brouard
 #if     defined(__bsd__)                /* get current working directory */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
       extern char       *getwd( );  
     Revision 1.140  2011/09/02 10:37:54  brouard
       if ( getwd( dirc ) == NULL ) {    Summary: times.h is ok with mingw32 now.
 #else  
       extern char       *getcwd( );    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.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.138  2010/04/30 18:19:40  brouard
       }    *** empty log message ***
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.137  2010/04/29 18:11:38  brouard
       s++;                              /* after this, the filename */    (Module): Checking covariates for more complex models
       l2 = strlen( s );                 /* length of filename */    than V1+V2. A lot of change to be done. Unstable.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.136  2010/04/26 20:30:53  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): merging some libgsl code. Fixing computation
       dirc[l1-l2] = 0;                  /* add zero */    of likelione (using inter/intrapolation if mle = 0) in order to
    }    get same likelihood as if mle=1.
    l1 = strlen( dirc );                 /* length of directory */    Some cleaning of code and comments added.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.135  2009/10/29 15:33:14  brouard
 #else    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.134  2009/10/29 13:18:53  brouard
    s = strrchr( name, '.' );            /* find last / */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.133  2009/07/06 10:21:25  brouard
    l1= strlen( name);    just nforces
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.132  2009/07/06 08:22:05  brouard
    finame[l1-l2]= 0;    Many tings
    return( 0 );                         /* we're done */  
 }    Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
   
 /******************************************/    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
 void replace(char *s, char*t)    lot of cleaning with variables initialized to 0. Trying to make
 {    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   int i;  
   int lg=20;    Revision 1.129  2007/08/31 13:49:27  lievre
   i=0;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.128  2006/06/30 13:02:05  brouard
     (s[i] = t[i]);    (Module): Clarifications on computing e.j
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.127  2006/04/28 18:11:50  brouard
 }    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 int nbocc(char *s, char occ)    loop. Now we define nhstepma in the age loop.
 {    (Module): In order to speed up (in case of numerous covariates) we
   int i,j=0;    compute health expectancies (without variances) in a first step
   int lg=20;    and then all the health expectancies with variances or standard
   i=0;    deviation (needs data from the Hessian matrices) which slows the
   lg=strlen(s);    computation.
   for(i=0; i<= lg; i++) {    In the future we should be able to stop the program is only health
   if  (s[i] == occ ) j++;    expectancies and graph are needed without standard deviations.
   }  
   return j;    Revision 1.126  2006/04/28 17:23:28  brouard
 }    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 void cutv(char *u,char *v, char*t, char occ)    loop. Now we define nhstepma in the age loop.
 {    Version 0.98h
   /* cuts string t into u and v where u is ended by char occ excluding it  
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    Revision 1.125  2006/04/04 15:20:31  lievre
      gives u="abcedf" and v="ghi2j" */    Errors in calculation of health expectancies. Age was not initialized.
   int i,lg,j,p=0;    Forecasting file added.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.124  2006/03/22 17:13:53  lievre
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Parameters are printed with %lf instead of %f (more numbers after the comma).
   }    The log-likelihood is printed in the log file
   
   lg=strlen(t);    Revision 1.123  2006/03/20 10:52:43  brouard
   for(j=0; j<p; j++) {    * imach.c (Module): <title> changed, corresponds to .htm file
     (u[j] = t[j]);    name. <head> headers where missing.
   }  
      u[p]='\0';    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
    for(j=0; j<= lg; j++) {    otherwise the weight is truncated).
     if (j>=(p+1))(v[j-p-1] = t[j]);    Modification of warning when the covariates values are not 0 or
   }    1.
 }    Version 0.98g
   
 /********************** nrerror ********************/    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 void nrerror(char error_text[])    English (a comma might work with a correct LC_NUMERIC environment,
 {    otherwise the weight is truncated).
   fprintf(stderr,"ERREUR ...\n");    Modification of warning when the covariates values are not 0 or
   fprintf(stderr,"%s\n",error_text);    1.
   exit(1);    Version 0.98g
 }  
 /*********************** vector *******************/    Revision 1.121  2006/03/16 17:45:01  lievre
 double *vector(int nl, int nh)    * imach.c (Module): Comments concerning covariates added
 {  
   double *v;    * imach.c (Module): refinements in the computation of lli if
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    status=-2 in order to have more reliable computation if stepm is
   if (!v) nrerror("allocation failure in vector");    not 1 month. Version 0.98f
   return v-nl+NR_END;  
 }    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 /************************ free vector ******************/    status=-2 in order to have more reliable computation if stepm is
 void free_vector(double*v, int nl, int nh)    not 1 month. Version 0.98f
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.119  2006/03/15 17:42:26  brouard
 }    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.118  2006/03/14 18:20:07  brouard
 {    (Module): varevsij Comments added explaining the second
   int *v;    table of variances if popbased=1 .
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   if (!v) nrerror("allocation failure in ivector");    (Module): Function pstamp added
   return v-nl+NR_END;    (Module): Version 0.98d
 }  
     Revision 1.117  2006/03/14 17:16:22  brouard
 /******************free ivector **************************/    (Module): varevsij Comments added explaining the second
 void free_ivector(int *v, long nl, long nh)    table of variances if popbased=1 .
 {    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   free((FREE_ARG)(v+nl-NR_END));    (Module): Function pstamp added
 }    (Module): Version 0.98d
   
 /******************* imatrix *******************************/    Revision 1.116  2006/03/06 10:29:27  brouard
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Module): Variance-covariance wrong links and
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    varian-covariance of ej. is needed (Saito).
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.115  2006/02/27 12:17:45  brouard
   int **m;    (Module): One freematrix added in mlikeli! 0.98c
    
   /* allocate pointers to rows */    Revision 1.114  2006/02/26 12:57:58  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Module): Some improvements in processing parameter
   if (!m) nrerror("allocation failure 1 in matrix()");    filename with strsep.
   m += NR_END;  
   m -= nrl;    Revision 1.113  2006/02/24 14:20:24  brouard
      (Module): Memory leaks checks with valgrind and:
      datafile was not closed, some imatrix were not freed and on matrix
   /* allocate rows and set pointers to them */    allocation too.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.112  2006/01/30 09:55:26  brouard
   m[nrl] += NR_END;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   m[nrl] -= ncl;  
      Revision 1.111  2006/01/25 20:38:18  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): Lots of cleaning and bugs added (Gompertz)
      (Module): Comments can be added in data file. Missing date values
   /* return pointer to array of pointers to rows */    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_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.109  2006/01/24 19:37:15  brouard
       int **m;    (Module): Comments (lines starting with a #) are allowed in data.
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.108  2006/01/19 18:05:42  lievre
 {    Gnuplot problem appeared...
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    To be fixed
   free((FREE_ARG) (m+nrl-NR_END));  
 }    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.106  2006/01/19 13:24:36  brouard
 {    Some cleaning and links added in html output
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.104  2005/09/30 16:11:43  lievre
   m += NR_END;    (Module): sump fixed, loop imx fixed, and simplifications.
   m -= nrl;    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (instead of missing=-1 in earlier versions) and his/her
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    contributions to the likelihood is 1 - Prob of dying from last
   m[nrl] += NR_END;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   m[nrl] -= ncl;    the healthy state at last known wave). Version is 0.98
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.103  2005/09/30 15:54:49  lievre
   return m;    (Module): sump fixed, loop imx fixed, and simplifications.
 }  
     Revision 1.102  2004/09/15 17:31:30  brouard
 /*************************free matrix ************************/    Add the possibility to read data file including tab characters.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.101  2004/09/15 10:38:38  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Fix on curr_time
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Revision 1.99  2004/06/05 08:57:40  brouard
 {    *** empty log message ***
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    directly from the data i.e. without the need of knowing the health
   if (!m) nrerror("allocation failure 1 in matrix()");    state at each age, but using a Gompertz model: log u =a + b*age .
   m += NR_END;    This is the basic analysis of mortality and should be done before any
   m -= nrl;    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    from other sources like vital statistic data.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    The same imach parameter file can be used but the option for mle should be -3.
   m[nrl] -= ncl;  
     Agnès, who wrote this part of the code, tried to keep most of the
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    former routines in order to include the new code within the former code.
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    The output is very simple: only an estimate of the intercept and of
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    the slope with 95% confident intervals.
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Current limitations:
   for (j=ncl+1; j<=nch; j++)    A) Even if you enter covariates, i.e. with the
     m[nrl][j]=m[nrl][j-1]+nlay;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
      B) There is no computation of Life Expectancy nor Life Table.
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Revision 1.97  2004/02/20 13:25:42  lievre
     for (j=ncl+1; j<=nch; j++)    Version 0.96d. Population forecasting command line is (temporarily)
       m[i][j]=m[i][j-1]+nlay;    suppressed.
   }  
   return m;    Revision 1.96  2003/07/15 15:38:55  brouard
 }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Revision 1.95  2003/07/08 07:54:34  brouard
 {    * imach.c (Repository):
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    (Repository): Using imachwizard code to output a more meaningful covariance
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    matrix (cov(a12,c31) instead of numbers.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 /***************** f1dim *************************/  
 extern int ncom;    Revision 1.93  2003/06/25 16:33:55  brouard
 extern double *pcom,*xicom;    (Module): On windows (cygwin) function asctime_r doesn't
 extern double (*nrfunc)(double []);    exist so I changed back to asctime which exists.
      (Module): Version 0.96b
 double f1dim(double x)  
 {    Revision 1.92  2003/06/25 16:30:45  brouard
   int j;    (Module): On windows (cygwin) function asctime_r doesn't
   double f;    exist so I changed back to asctime which exists.
   double *xt;  
      Revision 1.91  2003/06/25 15:30:29  brouard
   xt=vector(1,ncom);    * imach.c (Repository): Duplicated warning errors corrected.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    (Repository): Elapsed time after each iteration is now output. It
   f=(*nrfunc)(xt);    helps to forecast when convergence will be reached. Elapsed time
   free_vector(xt,1,ncom);    is stamped in powell.  We created a new html file for the graphs
   return f;    concerning matrix of covariance. It has extension -cov.htm.
 }  
     Revision 1.90  2003/06/24 12:34:15  brouard
 /*****************brent *************************/    (Module): Some bugs corrected for windows. Also, when
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   int iter;  
   double a,b,d,etemp;    Revision 1.89  2003/06/24 12:30:52  brouard
   double fu,fv,fw,fx;    (Module): Some bugs corrected for windows. Also, when
   double ftemp;    mle=-1 a template is output in file "or"mypar.txt with the design
   double p,q,r,tol1,tol2,u,v,w,x,xm;    of the covariance matrix to be input.
   double e=0.0;  
      Revision 1.88  2003/06/23 17:54:56  brouard
   a=(ax < cx ? ax : cx);    * 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.
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.87  2003/06/18 12:26:01  brouard
   fw=fv=fx=(*f)(x);    Version 0.96
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    Revision 1.86  2003/06/17 20:04:08  brouard
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    (Module): Change position of html and gnuplot routines and added
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    routine fileappend.
     printf(".");fflush(stdout);  
     fprintf(ficlog,".");fflush(ficlog);    Revision 1.85  2003/06/17 13:12:43  brouard
 #ifdef DEBUG    * imach.c (Repository): Check when date of death was earlier that
     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);    current date of interview. It may happen when the death was just
     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);    prior to the death. In this case, dh was negative and likelihood
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    was wrong (infinity). We still send an "Error" but patch by
 #endif    assuming that the date of death was just one stepm after the
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    interview.
       *xmin=x;    (Repository): Because some people have very long ID (first column)
       return fx;    we changed int to long in num[] and we added a new lvector for
     }    memory allocation. But we also truncated to 8 characters (left
     ftemp=fu;    truncation)
     if (fabs(e) > tol1) {    (Repository): No more line truncation errors.
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    Revision 1.84  2003/06/13 21:44:43  brouard
       p=(x-v)*q-(x-w)*r;    * imach.c (Repository): Replace "freqsummary" at a correct
       q=2.0*(q-r);    place. It differs from routine "prevalence" which may be called
       if (q > 0.0) p = -p;    many times. Probs is memory consuming and must be used with
       q=fabs(q);    parcimony.
       etemp=e;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    Revision 1.83  2003/06/10 13:39:11  lievre
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    *** empty log message ***
       else {  
         d=p/q;    Revision 1.82  2003/06/05 15:57:20  brouard
         u=x+d;    Add log in  imach.c and  fullversion number is now printed.
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  */
       }  /*
     } else {     Interpolated Markov Chain
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }    Short summary of the programme:
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    
     fu=(*f)(u);    This program computes Healthy Life Expectancies from
     if (fu <= fx) {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
       if (u >= x) a=x; else b=x;    first survey ("cross") where individuals from different ages are
       SHFT(v,w,x,u)    interviewed on their health status or degree of disability (in the
         SHFT(fv,fw,fx,fu)    case of a health survey which is our main interest) -2- at least a
         } else {    second wave of interviews ("longitudinal") which measure each change
           if (u < x) a=u; else b=u;    (if any) in individual health status.  Health expectancies are
           if (fu <= fw || w == x) {    computed from the time spent in each health state according to a
             v=w;    model. More health states you consider, more time is necessary to reach the
             w=u;    Maximum Likelihood of the parameters involved in the model.  The
             fv=fw;    simplest model is the multinomial logistic model where pij is the
             fw=fu;    probability to be observed in state j at the second wave
           } else if (fu <= fv || v == x || v == w) {    conditional to be observed in state i at the first wave. Therefore
             v=u;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
             fv=fu;    '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
         }    where the markup *Covariates have to be included here again* invites
   }    you to do it.  More covariates you add, slower the
   nrerror("Too many iterations in brent");    convergence.
   *xmin=x;  
   return fx;    The advantage of this computer programme, compared to a simple
 }    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 /****************** mnbrak ***********************/    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))    hPijx is the probability to be observed in state i at age x+h
 {    conditional to the observed state i at age x. The delay 'h' can be
   double ulim,u,r,q, dum;    split into an exact number (nh*stepm) of unobserved intermediate
   double fu;    states. This elementary transition (by month, quarter,
      semester or year) is modelled as a multinomial logistic.  The hPx
   *fa=(*func)(*ax);    matrix is simply the matrix product of nh*stepm elementary matrices
   *fb=(*func)(*bx);    and the contribution of each individual to the likelihood is simply
   if (*fb > *fa) {    hPijx.
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)    Also this programme outputs the covariance matrix of the parameters but also
       }    of the life expectancies. It also computes the period (stable) prevalence. 
   *cx=(*bx)+GOLD*(*bx-*ax);    
   *fc=(*func)(*cx);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   while (*fb > *fc) {             Institut national d'études démographiques, Paris.
     r=(*bx-*ax)*(*fb-*fc);    This software have been partly granted by Euro-REVES, a concerted action
     q=(*bx-*cx)*(*fb-*fa);    from the European Union.
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    It is copyrighted identically to a GNU software product, ie programme and
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    software can be distributed freely for non commercial use. Latest version
     ulim=(*bx)+GLIMIT*(*cx-*bx);    can be accessed at http://euroreves.ined.fr/imach .
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     } else if ((*cx-u)*(u-ulim) > 0.0) {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       fu=(*func)(u);    
       if (fu < *fc) {    **********************************************************************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /*
           SHFT(*fb,*fc,fu,(*func)(u))    main
           }    read parameterfile
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    read datafile
       u=ulim;    concatwav
       fu=(*func)(u);    freqsummary
     } else {    if (mle >= 1)
       u=(*cx)+GOLD*(*cx-*bx);      mlikeli
       fu=(*func)(u);    print results files
     }    if mle==1 
     SHFT(*ax,*bx,*cx,u)       computes hessian
       SHFT(*fa,*fb,*fc,fu)    read end of parameter file: agemin, agemax, bage, fage, estepm
       }        begin-prev-date,...
 }    open gnuplot file
     open html file
 /*************** linmin ************************/    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
      for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 int ncom;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 double *pcom,*xicom;      freexexit2 possible for memory heap.
 double (*nrfunc)(double []);  
      h Pij x                         | pij_nom  ficrestpij
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 {         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   double brent(double ax, double bx, double cx,         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
               double *fc, double (*func)(double));    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   int j;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   double xx,xmin,bx,ax;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   double fx,fb,fa;  
      forecasting if prevfcast==1 prevforecast call prevalence()
   ncom=n;    health expectancies
   pcom=vector(1,n);    Variance-covariance of DFLE
   xicom=vector(1,n);    prevalence()
   nrfunc=func;     movingaverage()
   for (j=1;j<=n;j++) {    varevsij() 
     pcom[j]=p[j];    if popbased==1 varevsij(,popbased)
     xicom[j]=xi[j];    total life expectancies
   }    Variance of period (stable) prevalence
   ax=0.0;   end
   xx=1.0;  */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define POWELL /* Instead of NLOPT */
 #ifdef DEBUG  /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /* #define MNBRAKORIGINAL */ /* Don't use mnbrak fix */
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  #include <math.h>
   for (j=1;j<=n;j++) {  #include <stdio.h>
     xi[j] *= xmin;  #include <stdlib.h>
     p[j] += xi[j];  #include <string.h>
   }  
   free_vector(xicom,1,n);  #ifdef _WIN32
   free_vector(pcom,1,n);  #include <io.h>
 }  #include <windows.h>
   #include <tchar.h>
 /*************** powell ************************/  #else
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #include <unistd.h>
             double (*func)(double []))  #endif
 {  
   void linmin(double p[], double xi[], int n, double *fret,  #include <limits.h>
               double (*func)(double []));  #include <sys/types.h>
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  #if defined(__GNUC__)
   double fp,fptt;  #include <sys/utsname.h> /* Doesn't work on Windows */
   double *xits;  #endif
   pt=vector(1,n);  
   ptt=vector(1,n);  #include <sys/stat.h>
   xit=vector(1,n);  #include <errno.h>
   xits=vector(1,n);  /* extern int errno; */
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  /* #ifdef LINUX */
   for (*iter=1;;++(*iter)) {  /* #include <time.h> */
     fp=(*fret);  /* #include "timeval.h" */
     ibig=0;  /* #else */
     del=0.0;  /* #include <sys/time.h> */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /* #endif */
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  #include <time.h>
       printf(" %d %.12f",i, p[i]);  
     fprintf(ficlog," %d %.12f",i, p[i]);  #ifdef GSL
     printf("\n");  #include <gsl/gsl_errno.h>
     fprintf(ficlog,"\n");  #include <gsl/gsl_multimin.h>
     for (i=1;i<=n;i++) {  #endif
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  
 #ifdef DEBUG  #ifdef NLOPT
       printf("fret=%lf \n",*fret);  #include <nlopt.h>
       fprintf(ficlog,"fret=%lf \n",*fret);  typedef struct {
 #endif    double (* function)(double [] );
       printf("%d",i);fflush(stdout);  } myfunc_data ;
       fprintf(ficlog,"%d",i);fflush(ficlog);  #endif
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  /* #include <libintl.h> */
         del=fabs(fptt-(*fret));  /* #define _(String) gettext (String) */
         ibig=i;  
       }  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  #define GNUPLOTPROGRAM "gnuplot"
       fprintf(ficlog,"%d %.12e",i,(*fret));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       for (j=1;j<=n;j++) {  #define FILENAMELENGTH 132
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       }  
       for(j=1;j<=n;j++) {  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         printf(" p=%.12e",p[j]);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
         fprintf(ficlog," p=%.12e",p[j]);  
       }  #define NINTERVMAX 8
       printf("\n");  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       fprintf(ficlog,"\n");  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #endif  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
     }  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define MAXN 20000
 #ifdef DEBUG  #define YEARM 12. /**< Number of months per year */
       int k[2],l;  #define AGESUP 130
       k[0]=1;  #define AGEBASE 40
       k[1]=-1;  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
       printf("Max: %.12e",(*func)(p));  #ifdef _WIN32
       fprintf(ficlog,"Max: %.12e",(*func)(p));  #define DIRSEPARATOR '\\'
       for (j=1;j<=n;j++) {  #define CHARSEPARATOR "\\"
         printf(" %.12e",p[j]);  #define ODIRSEPARATOR '/'
         fprintf(ficlog," %.12e",p[j]);  #else
       }  #define DIRSEPARATOR '/'
       printf("\n");  #define CHARSEPARATOR "/"
       fprintf(ficlog,"\n");  #define ODIRSEPARATOR '\\'
       for(l=0;l<=1;l++) {  #endif
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /* $Id$ */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  /* $State$ */
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  char fullversion[]="$Revision$ $Date$"; 
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  char strstart[80];
       }  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 #endif  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int nvar=0, nforce=0; /* Number of variables, number of forces */
   /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       free_vector(xit,1,n);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
       free_vector(xits,1,n);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
       free_vector(ptt,1,n);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       free_vector(pt,1,n);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       return;  int cptcovprodnoage=0; /**< Number of covariate products without age */   
     }  int cptcoveff=0; /* Total number of covariates to vary for printing results */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  int cptcov=0; /* Working variable */
     for (j=1;j<=n;j++) {  int npar=NPARMAX;
       ptt[j]=2.0*p[j]-pt[j];  int nlstate=2; /* Number of live states */
       xit[j]=p[j]-pt[j];  int ndeath=1; /* Number of dead states */
       pt[j]=p[j];  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     }  int popbased=0;
     fptt=(*func)(ptt);  
     if (fptt < fp) {  int *wav; /* Number of waves for this individuual 0 is possible */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  int maxwav=0; /* Maxim number of waves */
       if (t < 0.0) {  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
         linmin(p,xit,n,fret,func);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
         for (j=1;j<=n;j++) {  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
           xi[j][ibig]=xi[j][n];                     to the likelihood and the sum of weights (done by funcone)*/
           xi[j][n]=xit[j];  int mle=1, weightopt=0;
         }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #ifdef DEBUG  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
         for(j=1;j<=n;j++){  int countcallfunc=0;  /* Count the number of calls to func */
           printf(" %.12e",xit[j]);  double jmean=1; /* Mean space between 2 waves */
           fprintf(ficlog," %.12e",xit[j]);  double **matprod2(); /* test */
         }  double **oldm, **newm, **savm; /* Working pointers to matrices */
         printf("\n");  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
         fprintf(ficlog,"\n");  /*FILE *fic ; */ /* Used in readdata only */
 #endif  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       }  FILE *ficlog, *ficrespow;
     }  int globpr=0; /* Global variable for printing or not */
   }  double fretone; /* Only one call to likelihood */
 }  long ipmx=0; /* Number of contributions */
   double sw; /* Sum of weights */
 /**** Prevalence limit ****************/  char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  FILE *ficresilk;
 {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  FILE *ficresprobmorprev;
      matrix by transitions matrix until convergence is reached */  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
   int i, ii,j,k;  char filerese[FILENAMELENGTH];
   double min, max, maxmin, maxmax,sumnew=0.;  FILE *ficresstdeij;
   double **matprod2();  char fileresstde[FILENAMELENGTH];
   double **out, cov[NCOVMAX], **pmij();  FILE *ficrescveij;
   double **newm;  char filerescve[FILENAMELENGTH];
   double agefin, delaymax=50 ; /* Max number of years to converge */  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
   for (ii=1;ii<=nlstate+ndeath;ii++)  FILE  *ficresvpl;
     for (j=1;j<=nlstate+ndeath;j++){  char fileresvpl[FILENAMELENGTH];
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char title[MAXLINE];
     }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
    cov[1]=1.;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
    char command[FILENAMELENGTH];
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int  outcmd=0;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     /* Covariates have to be included here again */  
      cov[2]=agefin;  char filelog[FILENAMELENGTH]; /* Log file */
    char filerest[FILENAMELENGTH];
       for (k=1; k<=cptcovn;k++) {  char fileregp[FILENAMELENGTH];
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char popfile[FILENAMELENGTH];
         /*      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]]);*/  
       }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /* struct timezone tzp; */
   /* extern int gettimeofday(); */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  struct tm tml, *gmtime(), *localtime();
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  extern time_t time();
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   struct tm start_time, end_time, curr_time, last_time, forecast_time;
     savm=oldm;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     oldm=newm;  struct tm tm;
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  char strcurr[80], strfor[80];
       min=1.;  
       max=0.;  char *endptr;
       for(i=1; i<=nlstate; i++) {  long lval;
         sumnew=0;  double dval;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  #define NR_END 1
         max=FMAX(max,prlim[i][j]);  #define FREE_ARG char*
         min=FMIN(min,prlim[i][j]);  #define FTOL 1.0e-10
       }  
       maxmin=max-min;  #define NRANSI 
       maxmax=FMAX(maxmax,maxmin);  #define ITMAX 200 
     }  
     if(maxmax < ftolpl){  #define TOL 2.0e-4 
       return prlim;  
     }  #define CGOLD 0.3819660 
   }  #define ZEPS 1.0e-10 
 }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 /*************** transition probabilities ***************/  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #define TINY 1.0e-20 
 {  
   double s1, s2;  static double maxarg1,maxarg2;
   /*double t34;*/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   int i,j,j1, nc, ii, jj;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
     for(i=1; i<= nlstate; i++){  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     for(j=1; j<i;j++){  #define rint(a) floor(a+0.5)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
         /*s2 += param[i][j][nc]*cov[nc];*/  #define mytinydouble 1.0e-16
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
       }  /* static double dsqrarg; */
       ps[i][j]=s2;  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  static double sqrarg;
     }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     for(j=i+1; j<=nlstate+ndeath;j++){  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int agegomp= AGEGOMP;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  int imx; 
       }  int stepm=1;
       ps[i][j]=s2;  /* Stepm, step in month: minimum step interpolation*/
     }  
   }  int estepm;
     /*ps[3][2]=1;*/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
   for(i=1; i<= nlstate; i++){  int m,nb;
      s1=0;  long *num;
     for(j=1; j<i; j++)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       s1+=exp(ps[i][j]);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     for(j=i+1; j<=nlstate+ndeath; j++)  double **pmmij, ***probs;
       s1+=exp(ps[i][j]);  double *ageexmed,*agecens;
     ps[i][i]=1./(s1+1.);  double dateintmean=0;
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double *weight;
     for(j=i+1; j<=nlstate+ndeath; j++)  int **s; /* Status */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double *agedc;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   } /* end i */                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  double  idx; 
     for(jj=1; jj<= nlstate+ndeath; jj++){  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       ps[ii][jj]=0;  int *Ndum; /** Freq of modality (tricode */
       ps[ii][ii]=1;  int **codtab; /**< codtab=imatrix(1,100,1,10); */
     }  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   }  double *lsurv, *lpop, *tpop;
   
   double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  double ftolhess; /**< Tolerance for computing hessian */
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /**************** split *************************/
    }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     printf("\n ");  {
     }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     printf("\n ");printf("%lf ",cov[2]);*/       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 /*    */ 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    char  *ss;                            /* pointer */
   goto end;*/    int   l1, l2;                         /* length counters */
     return ps;  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 /**************** Product of 2 matrices ******************/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so determine current directory */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      strcpy( name, path );               /* we got the fullname name because no directory */
 {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      /* get current working directory */
   /* in, b, out are matrice of pointers which should have been initialized      /*    extern  char* getcwd ( char *buf , int len);*/
      before: only the contents of out is modified. The function returns  #ifdef WIN32
      a pointer to pointers identical to out */      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
   long i, j, k;  #else
   for(i=nrl; i<= nrh; i++)          if (getcwd(dirc, FILENAME_MAX) == NULL) {
     for(k=ncolol; k<=ncoloh; k++)  #endif
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        return( GLOCK_ERROR_GETCWD );
         out[i][k] +=in[i][j]*b[j][k];      }
       /* got dirc from getcwd*/
   return out;      printf(" DIRC = %s \n",dirc);
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 /************* Higher Matrix Product ***************/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      printf(" DIRC2 = %s \n",dirc);
      duration (i.e. until    }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    /* We add a separator at the end of dirc if not exists */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    l1 = strlen( dirc );                  /* length of directory */
      (typically every 2 years instead of every month which is too big).    if( dirc[l1-1] != DIRSEPARATOR ){
      Model is determined by parameters x and covariates have to be      dirc[l1] =  DIRSEPARATOR;
      included manually here.      dirc[l1+1] = 0; 
       printf(" DIRC3 = %s \n",dirc);
      */    }
     ss = strrchr( name, '.' );            /* find last / */
   int i, j, d, h, k;    if (ss >0){
   double **out, cov[NCOVMAX];      ss++;
   double **newm;      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
   /* Hstepm could be zero and should return the unit matrix */      l2= strlen(ss)+1;
   for (i=1;i<=nlstate+ndeath;i++)      strncpy( finame, name, l1-l2);
     for (j=1;j<=nlstate+ndeath;j++){      finame[l1-l2]= 0;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    }
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }    return( 0 );                          /* we're done */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  
       newm=savm;  /******************************************/
       /* Covariates have to be included here again */  
       cov[1]=1.;  void replace_back_to_slash(char *s, char*t)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    int i;
       for (k=1; k<=cptcovage;k++)    int lg=0;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    i=0;
       for (k=1; k<=cptcovprod;k++)    lg=strlen(t);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  }
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  char *trimbb(char *out, char *in)
       savm=oldm;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       oldm=newm;    char *s;
     }    s=out;
     for(i=1; i<=nlstate+ndeath; i++)    while (*in != '\0'){
       for(j=1;j<=nlstate+ndeath;j++) {      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         po[i][j][h]=newm[i][j];        in++;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      }
          */      *out++ = *in++;
       }    }
   } /* end h */    *out='\0';
   return po;    return s;
 }  }
   
   char *cutl(char *blocc, char *alocc, char *in, char occ)
 /*************** log-likelihood *************/  {
 double func( double *x)    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
 {       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   int i, ii, j, k, mi, d, kk;       gives blocc="abcdef2ghi" and alocc="j".
   double l, ll[NLSTATEMAX], cov[NCOVMAX];       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   double **out;    */
   double sw; /* Sum of weights */    char *s, *t;
   double lli; /* Individual log likelihood */    t=in;s=in;
   long ipmx;    while ((*in != occ) && (*in != '\0')){
   /*extern weight */      *alocc++ = *in++;
   /* We are differentiating ll according to initial status */    }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    if( *in == occ){
   /*for(i=1;i<imx;i++)      *(alocc)='\0';
     printf(" %d\n",s[4][i]);      s=++in;
   */    }
   cov[1]=1.;   
     if (s == t) {/* occ not found */
   for(k=1; k<=nlstate; k++) ll[k]=0.;      *(alocc-(in-s))='\0';
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      in=s;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    }
     for(mi=1; mi<= wav[i]-1; mi++){    while ( *in != '\0'){
       for (ii=1;ii<=nlstate+ndeath;ii++)      *blocc++ = *in++;
         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;    *blocc='\0';
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return t;
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  char *cutv(char *blocc, char *alocc, char *in, char occ)
         }  {
            /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       gives blocc="abcdef2ghi" and alocc="j".
         savm=oldm;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         oldm=newm;    */
            char *s, *t;
            t=in;s=in;
       } /* end mult */    while (*in != '\0'){
            while( *in == occ){
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        *blocc++ = *in++;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        s=in;
       ipmx +=1;      }
       sw += weight[i];      *blocc++ = *in++;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    }
     } /* end of wave */    if (s == t) /* occ not found */
   } /* end of individual */      *(blocc-(in-s))='\0';
     else
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      *(blocc-(in-s)-1)='\0';
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    in=s;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    while ( *in != '\0'){
   return -l;      *alocc++ = *in++;
 }    }
   
     *alocc='\0';
 /*********** Maximum Likelihood Estimation ***************/    return s;
   }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  int nbocc(char *s, char occ)
   int i,j, iter;  {
   double **xi,*delti;    int i,j=0;
   double fret;    int lg=20;
   xi=matrix(1,npar,1,npar);    i=0;
   for (i=1;i<=npar;i++)    lg=strlen(s);
     for (j=1;j<=npar;j++)    for(i=0; i<= lg; i++) {
       xi[i][j]=(i==j ? 1.0 : 0.0);    if  (s[i] == occ ) j++;
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    }
   powell(p,xi,npar,ftol,&iter,&fret,func);    return j;
   }
    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));  /* void cutv(char *u,char *v, char*t, char occ) */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /* { */
   /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
 }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /*      gives u="abcdef2ghi" and v="j" *\/ */
 /**** Computes Hessian and covariance matrix ***/  /*   int i,lg,j,p=0; */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*   i=0; */
 {  /*   lg=strlen(t); */
   double  **a,**y,*x,pd;  /*   for(j=0; j<=lg-1; j++) { */
   double **hess;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   int i, j,jk;  /*   } */
   int *indx;  
   /*   for(j=0; j<p; j++) { */
   double hessii(double p[], double delta, int theta, double delti[]);  /*     (u[j] = t[j]); */
   double hessij(double p[], double delti[], int i, int j);  /*   } */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  /*      u[p]='\0'; */
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   /*    for(j=0; j<= lg; j++) { */
   hess=matrix(1,npar,1,npar);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   printf("\nCalculation of the hessian matrix. Wait...\n");  /* } */
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  #ifdef _WIN32
     printf("%d",i);fflush(stdout);  char * strsep(char **pp, const char *delim)
     fprintf(ficlog,"%d",i);fflush(ficlog);  {
     hess[i][i]=hessii(p,ftolhess,i,delti);    char *p, *q;
     /*printf(" %f ",p[i]);*/           
     /*printf(" %lf ",hess[i][i]);*/    if ((p = *pp) == NULL)
   }      return 0;
      if ((q = strpbrk (p, delim)) != NULL)
   for (i=1;i<=npar;i++) {    {
     for (j=1;j<=npar;j++)  {      *pp = q + 1;
       if (j>i) {      *q = '\0';
         printf(".%d%d",i,j);fflush(stdout);    }
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    else
         hess[i][j]=hessij(p,delti,i,j);      *pp = 0;
         hess[j][i]=hess[i][j];        return p;
         /*printf(" %lf ",hess[i][j]);*/  }
       }  #endif
     }  
   }  /********************** nrerror ********************/
   printf("\n");  
   fprintf(ficlog,"\n");  void nrerror(char error_text[])
   {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    fprintf(stderr,"ERREUR ...\n");
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    fprintf(stderr,"%s\n",error_text);
      exit(EXIT_FAILURE);
   a=matrix(1,npar,1,npar);  }
   y=matrix(1,npar,1,npar);  /*********************** vector *******************/
   x=vector(1,npar);  double *vector(int nl, int nh)
   indx=ivector(1,npar);  {
   for (i=1;i<=npar;i++)    double *v;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   ludcmp(a,npar,indx,&pd);    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   for (j=1;j<=npar;j++) {  }
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  /************************ free vector ******************/
     lubksb(a,npar,indx,x);  void free_vector(double*v, int nl, int nh)
     for (i=1;i<=npar;i++){  {
       matcov[i][j]=x[i];    free((FREE_ARG)(v+nl-NR_END));
     }  }
   }  
   /************************ivector *******************************/
   printf("\n#Hessian matrix#\n");  int *ivector(long nl,long nh)
   fprintf(ficlog,"\n#Hessian matrix#\n");  {
   for (i=1;i<=npar;i++) {    int *v;
     for (j=1;j<=npar;j++) {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       printf("%.3e ",hess[i][j]);    if (!v) nrerror("allocation failure in ivector");
       fprintf(ficlog,"%.3e ",hess[i][j]);    return v-nl+NR_END;
     }  }
     printf("\n");  
     fprintf(ficlog,"\n");  /******************free ivector **************************/
   }  void free_ivector(int *v, long nl, long nh)
   {
   /* Recompute Inverse */    free((FREE_ARG)(v+nl-NR_END));
   for (i=1;i<=npar;i++)  }
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);  /************************lvector *******************************/
   long *lvector(long nl,long nh)
   /*  printf("\n#Hessian matrix recomputed#\n");  {
     long *v;
   for (j=1;j<=npar;j++) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     for (i=1;i<=npar;i++) x[i]=0;    if (!v) nrerror("allocation failure in ivector");
     x[j]=1;    return v-nl+NR_END;
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  /******************free lvector **************************/
       printf("%.3e ",y[i][j]);  void free_lvector(long *v, long nl, long nh)
       fprintf(ficlog,"%.3e ",y[i][j]);  {
     }    free((FREE_ARG)(v+nl-NR_END));
     printf("\n");  }
     fprintf(ficlog,"\n");  
   }  /******************* imatrix *******************************/
   */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   free_matrix(a,1,npar,1,npar);  { 
   free_matrix(y,1,npar,1,npar);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   free_vector(x,1,npar);    int **m; 
   free_ivector(indx,1,npar);    
   free_matrix(hess,1,npar,1,npar);    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 }    m += NR_END; 
     m -= nrl; 
 /*************** hessian matrix ****************/    
 double hessii( double x[], double delta, int theta, double delti[])    
 {    /* allocate rows and set pointers to them */ 
   int i;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   int l=1, lmax=20;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double k1,k2;    m[nrl] += NR_END; 
   double p2[NPARMAX+1];    m[nrl] -= ncl; 
   double res;    
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   double fx;    
   int k=0,kmax=10;    /* return pointer to array of pointers to rows */ 
   double l1;    return m; 
   } 
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];  /****************** free_imatrix *************************/
   for(l=0 ; l <=lmax; l++){  void free_imatrix(m,nrl,nrh,ncl,nch)
     l1=pow(10,l);        int **m;
     delts=delt;        long nch,ncl,nrh,nrl; 
     for(k=1 ; k <kmax; k=k+1){       /* free an int matrix allocated by imatrix() */ 
       delt = delta*(l1*k);  { 
       p2[theta]=x[theta] +delt;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       k1=func(p2)-fx;    free((FREE_ARG) (m+nrl-NR_END)); 
       p2[theta]=x[theta]-delt;  } 
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */  /******************* matrix *******************************/
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  double **matrix(long nrl, long nrh, long ncl, long nch)
        {
 #ifdef DEBUG    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       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 **m;
       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    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    if (!m) nrerror("allocation failure 1 in matrix()");
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    m += NR_END;
         k=kmax;    m -= nrl;
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         k=kmax; l=lmax*10.;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       }    m[nrl] += NR_END;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    m[nrl] -= ncl;
         delts=delt;  
       }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
   }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   delti[theta]=delts;  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   return res;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
       */
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  /*************************free matrix ************************/
 {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   int i;  {
   int l=1, l1, lmax=20;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double k1,k2,k3,k4,res,fx;    free((FREE_ARG)(m+nrl-NR_END));
   double p2[NPARMAX+1];  }
   int k;  
   /******************* ma3x *******************************/
   fx=func(x);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (k=1; k<=2; k++) {  {
     for (i=1;i<=npar;i++) p2[i]=x[i];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     p2[thetai]=x[thetai]+delti[thetai]/k;    double ***m;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      if (!m) nrerror("allocation failure 1 in matrix()");
     p2[thetai]=x[thetai]+delti[thetai]/k;    m += NR_END;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    m -= nrl;
     k2=func(p2)-fx;  
      m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     p2[thetai]=x[thetai]-delti[thetai]/k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    m[nrl] += NR_END;
     k3=func(p2)-fx;    m[nrl] -= ncl;
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 #ifdef DEBUG    m[nrl][ncl] += NR_END;
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    m[nrl][ncl] -= nll;
     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);    for (j=ncl+1; j<=nch; j++) 
 #endif      m[nrl][j]=m[nrl][j-1]+nlay;
   }    
   return res;    for (i=nrl+1; i<=nrh; i++) {
 }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
 /************** Inverse of matrix **************/        m[i][j]=m[i][j-1]+nlay;
 void ludcmp(double **a, int n, int *indx, double *d)    }
 {    return m; 
   int i,imax,j,k;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   double big,dum,sum,temp;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   double *vv;    */
    }
   vv=vector(1,n);  
   *d=1.0;  /*************************free ma3x ************************/
   for (i=1;i<=n;i++) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     big=0.0;  {
     for (j=1;j<=n;j++)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       if ((temp=fabs(a[i][j])) > big) big=temp;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    free((FREE_ARG)(m+nrl-NR_END));
     vv[i]=1.0/big;  }
   }  
   for (j=1;j<=n;j++) {  /*************** function subdirf ***********/
     for (i=1;i<j;i++) {  char *subdirf(char fileres[])
       sum=a[i][j];  {
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    /* Caution optionfilefiname is hidden */
       a[i][j]=sum;    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/"); /* Add to the right */
     big=0.0;    strcat(tmpout,fileres);
     for (i=j;i<=n;i++) {    return tmpout;
       sum=a[i][j];  }
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  /*************** function subdirf2 ***********/
       a[i][j]=sum;  char *subdirf2(char fileres[], char *preop)
       if ( (dum=vv[i]*fabs(sum)) >= big) {  {
         big=dum;    
         imax=i;    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
     if (j != imax) {    strcat(tmpout,preop);
       for (k=1;k<=n;k++) {    strcat(tmpout,fileres);
         dum=a[imax][k];    return tmpout;
         a[imax][k]=a[j][k];  }
         a[j][k]=dum;  
       }  /*************** function subdirf3 ***********/
       *d = -(*d);  char *subdirf3(char fileres[], char *preop, char *preop2)
       vv[imax]=vv[j];  {
     }    
     indx[j]=imax;    /* Caution optionfilefiname is hidden */
     if (a[j][j] == 0.0) a[j][j]=TINY;    strcpy(tmpout,optionfilefiname);
     if (j != n) {    strcat(tmpout,"/");
       dum=1.0/(a[j][j]);    strcat(tmpout,preop);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    strcat(tmpout,preop2);
     }    strcat(tmpout,fileres);
   }    return tmpout;
   free_vector(vv,1,n);  /* Doesn't work */  }
 ;  
 }  char *asc_diff_time(long time_sec, char ascdiff[])
   {
 void lubksb(double **a, int n, int *indx, double b[])    long sec_left, days, hours, minutes;
 {    days = (time_sec) / (60*60*24);
   int i,ii=0,ip,j;    sec_left = (time_sec) % (60*60*24);
   double sum;    hours = (sec_left) / (60*60) ;
      sec_left = (sec_left) %(60*60);
   for (i=1;i<=n;i++) {    minutes = (sec_left) /60;
     ip=indx[i];    sec_left = (sec_left) % (60);
     sum=b[ip];    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     b[ip]=b[i];    return ascdiff;
     if (ii)  }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  /***************** f1dim *************************/
     b[i]=sum;  extern int ncom; 
   }  extern double *pcom,*xicom;
   for (i=n;i>=1;i--) {  extern double (*nrfunc)(double []); 
     sum=b[i];   
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  double f1dim(double x) 
     b[i]=sum/a[i][i];  { 
   }    int j; 
 }    double f;
     double *xt; 
 /************ Frequencies ********************/   
 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)    xt=vector(1,ncom); 
 {  /* Some frequencies */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
      f=(*nrfunc)(xt); 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    free_vector(xt,1,ncom); 
   int first;    return f; 
   double ***freq; /* Frequencies */  } 
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  /*****************brent *************************/
   FILE *ficresp;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   char fileresp[FILENAMELENGTH];  { 
      int iter; 
   pp=vector(1,nlstate);    double a,b,d,etemp;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    double fu=0,fv,fw,fx;
   strcpy(fileresp,"p");    double ftemp=0.;
   strcat(fileresp,fileres);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double e=0.0; 
     printf("Problem with prevalence resultfile: %s\n", fileresp);   
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    a=(ax < cx ? ax : cx); 
     exit(0);    b=(ax > cx ? ax : cx); 
   }    x=w=v=bx; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    fw=fv=fx=(*f)(x); 
   j1=0;    for (iter=1;iter<=ITMAX;iter++) { 
        xm=0.5*(a+b); 
   j=cptcoveff;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
   first=1;      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUGBRENT
   for(k1=1; k1<=j;k1++){      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(i1=1; i1<=ncodemax[k1];i1++){      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);
       j1++;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  #endif
         scanf("%d", i);*/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       for (i=-1; i<=nlstate+ndeath; i++)          *xmin=x; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          return fx; 
           for(m=agemin; m <= agemax+3; m++)      } 
             freq[i][jk][m]=0;      ftemp=fu;
            if (fabs(e) > tol1) { 
       dateintsum=0;        r=(x-w)*(fx-fv); 
       k2cpt=0;        q=(x-v)*(fx-fw); 
       for (i=1; i<=imx; i++) {        p=(x-v)*q-(x-w)*r; 
         bool=1;        q=2.0*(q-r); 
         if  (cptcovn>0) {        if (q > 0.0) p = -p; 
           for (z1=1; z1<=cptcoveff; z1++)        q=fabs(q); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        etemp=e; 
               bool=0;        e=d; 
         }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         if (bool==1) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           for(m=firstpass; m<=lastpass; m++){        else { 
             k2=anint[m][i]+(mint[m][i]/12.);          d=p/q; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          u=x+d; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;          if (u-a < tol2 || b-u < tol2) 
               if(agev[m][i]==1) agev[m][i]=agemax+2;            d=SIGN(tol1,xm-x); 
               if (m<lastpass) {        } 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      } else { 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
               }      } 
                    u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      fu=(*f)(u); 
                 dateintsum=dateintsum+k2;      if (fu <= fx) { 
                 k2cpt++;        if (u >= x) a=x; else b=x; 
               }        SHFT(v,w,x,u) 
             }        SHFT(fv,fw,fx,fu) 
           }      } else { 
         }        if (u < x) a=u; else b=u; 
       }        if (fu <= fw || w == x) { 
                  v=w; 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          w=u; 
           fv=fw; 
       if  (cptcovn>0) {          fw=fu; 
         fprintf(ficresp, "\n#********** Variable ");        } else if (fu <= fv || v == x || v == w) { 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          v=u; 
         fprintf(ficresp, "**********\n#");          fv=fu; 
       }        } 
       for(i=1; i<=nlstate;i++)      } 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    } 
       fprintf(ficresp, "\n");    nrerror("Too many iterations in brent"); 
          *xmin=x; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){    return fx; 
         if(i==(int)agemax+3){  } 
           fprintf(ficlog,"Total");  
         }else{  /****************** mnbrak ***********************/
           if(first==1){  
             first=0;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
             printf("See log file for details...\n");              double (*func)(double)) 
           }  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
           fprintf(ficlog,"Age %d", i);  the downhill direction (defined by the function as evaluated at the initial points) and returns
         }  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
         for(jk=1; jk <=nlstate ; jk++){  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)     */
             pp[jk] += freq[jk][m][i];    double ulim,u,r,q, dum;
         }    double fu; 
         for(jk=1; jk <=nlstate ; jk++){   
           for(m=-1, pos=0; m <=0 ; m++)    *fa=(*func)(*ax); 
             pos += freq[jk][m][i];    *fb=(*func)(*bx); 
           if(pp[jk]>=1.e-10){    if (*fb > *fa) { 
             if(first==1){      SHFT(dum,*ax,*bx,dum) 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      SHFT(dum,*fb,*fa,dum) 
             }    } 
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    *cx=(*bx)+GOLD*(*bx-*ax); 
           }else{    *fc=(*func)(*cx); 
             if(first==1)  #ifdef DEBUG
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
           }  #endif
         }    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
       r=(*bx-*ax)*(*fb-*fc); 
         for(jk=1; jk <=nlstate ; jk++){      q=(*bx-*cx)*(*fb-*fa); 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
             pp[jk] += freq[jk][m][i];        (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 */
       if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
         for(jk=1,pos=0; jk <=nlstate ; jk++)        fu=(*func)(u); 
           pos += pp[jk];  #ifdef DEBUG
         for(jk=1; jk <=nlstate ; jk++){        /* f(x)=A(x-u)**2+f(u) */
           if(pos>=1.e-5){        double A, fparabu; 
             if(first==1)        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        fparabu= *fa - A*(*ax-u)*(*ax-u);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        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);
           }else{        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
             if(first==1)        /* And thus,it can be that fu > *fc even if fparabu < *fc */
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
           }        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
           if( i <= (int) agemax){  #endif 
             if(pos>=1.e-5){  #ifdef MNBRAKORIGINAL
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  #else
               probs[i][jk][j1]= pp[jk]/pos;        if (fu > *fc) {
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  #ifdef DEBUG
             }        printf("mnbrak4  fu > fc \n");
             else        fprintf(ficlog, "mnbrak4 fu > fc\n");
               fprintf(ficresp," %d NaNq %.0f %.0f",i,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 *\/ */
                  dum=u; /* Shifting c and u */
         for(jk=-1; jk <=nlstate+ndeath; jk++)          u = *cx;
           for(m=-1; m <=nlstate+ndeath; m++)          *cx = dum;
             if(freq[jk][m][i] !=0 ) {          dum = fu;
             if(first==1)          fu = *fc;
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          *fc =dum;
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);        } else { /* end */
             }  #ifdef DEBUG
         if(i <= (int) agemax)        printf("mnbrak3  fu < fc \n");
           fprintf(ficresp,"\n");        fprintf(ficlog, "mnbrak3 fu < fc\n");
         if(first==1)  #endif
           printf("Others in log...\n");          dum=u; /* Shifting c and u */
         fprintf(ficlog,"\n");          u = *cx;
       }          *cx = dum;
     }          dum = fu;
   }          fu = *fc;
   dateintmean=dateintsum/k2cpt;          *fc =dum;
          }
   fclose(ficresp);  #endif
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   free_vector(pp,1,nlstate);  #ifdef DEBUG
          printf("mnbrak2  u after c but before ulim\n");
   /* End of Freq */        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
 }  #endif
         fu=(*func)(u); 
 /************ Prevalence ********************/        if (fu < *fc) { 
 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)  #ifdef DEBUG
 {  /* Some frequencies */        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
          fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  #endif
   double ***freq; /* Frequencies */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double *pp;          SHFT(*fb,*fc,fu,(*func)(u)) 
   double pos, k2;        } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   pp=vector(1,nlstate);  #ifdef DEBUG
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
          fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  #endif
   j1=0;        u=ulim; 
          fu=(*func)(u); 
   j=cptcoveff;      } else { /* u could be left to b (if r > q parabola has a maximum) */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  #ifdef DEBUG
          printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
   for(k1=1; k1<=j;k1++){        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
     for(i1=1; i1<=ncodemax[k1];i1++){  #endif
       j1++;        u=(*cx)+GOLD*(*cx-*bx); 
              fu=(*func)(u); 
       for (i=-1; i<=nlstate+ndeath; i++)        } /* end tests */
         for (jk=-1; jk<=nlstate+ndeath; jk++)        SHFT(*ax,*bx,*cx,u) 
           for(m=agemin; m <= agemax+3; m++)      SHFT(*fa,*fb,*fc,fu) 
             freq[i][jk][m]=0;  #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);
         bool=1;  #endif
         if  (cptcovn>0) {    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
           for (z1=1; z1<=cptcoveff; z1++)  } 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  /*************** linmin ************************/
         }  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         if (bool==1) {  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
           for(m=firstpass; m<=lastpass; m++){  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
             k2=anint[m][i]+(mint[m][i]/12.);  the value of func at the returned location p . This is actually all accomplished by calling the
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  routines mnbrak and brent .*/
               if(agev[m][i]==0) agev[m][i]=agemax+1;  int ncom; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;  double *pcom,*xicom;
               if (m<lastpass) {  double (*nrfunc)(double []); 
                 if (calagedate>0)   
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
                 else  { 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double brent(double ax, double bx, double cx, 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];                 double (*f)(double), double tol, double *xmin); 
               }    double f1dim(double x); 
             }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
           }                double *fc, double (*func)(double)); 
         }    int j; 
       }    double xx,xmin,bx,ax; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){    double fx,fb,fa;
         for(jk=1; jk <=nlstate ; jk++){   
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    ncom=n; 
             pp[jk] += freq[jk][m][i];    pcom=vector(1,n); 
         }    xicom=vector(1,n); 
         for(jk=1; jk <=nlstate ; jk++){    nrfunc=func; 
           for(m=-1, pos=0; m <=0 ; m++)    for (j=1;j<=n;j++) { 
             pos += freq[jk][m][i];      pcom[j]=p[j]; 
         }      xicom[j]=xi[j]; 
            } 
         for(jk=1; jk <=nlstate ; jk++){    ax=0.0; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    xx=1.0; 
             pp[jk] += freq[jk][m][i];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
         }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
          #ifdef DEBUG
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
            fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         for(jk=1; jk <=nlstate ; jk++){      #endif
           if( i <= (int) agemax){    for (j=1;j<=n;j++) { 
             if(pos>=1.e-5){      xi[j] *= xmin; 
               probs[i][jk][j1]= pp[jk]/pos;      p[j] += xi[j]; 
             }    } 
           }    free_vector(xicom,1,n); 
         }/* end jk */    free_vector(pcom,1,n); 
       }/* end i */  } 
     } /* end i1 */  
   } /* end k1 */  
   /*************** powell ************************/
    /*
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  Minimization of a function func of n variables. Input consists of an initial starting point
   free_vector(pp,1,nlstate);  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
 }  /* End of Freq */  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
 /************* Waves Concatenation ***************/  function value at p , and iter is the number of iterations taken. The routine linmin is used.
    */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 {              double (*func)(double [])) 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  { 
      Death is a valid wave (if date is known).    void linmin(double p[], double xi[], int n, double *fret, 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i                double (*func)(double [])); 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    int i,ibig,j; 
      and mw[mi+1][i]. dh depends on stepm.    double del,t,*pt,*ptt,*xit;
      */    double directest;
     double fp,fptt;
   int i, mi, m;    double *xits;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    int niterf, itmp;
      double sum=0., jmean=0.;*/  
   int first;    pt=vector(1,n); 
   int j, k=0,jk, ju, jl;    ptt=vector(1,n); 
   double sum=0.;    xit=vector(1,n); 
   first=0;    xits=vector(1,n); 
   jmin=1e+5;    *fret=(*func)(p); 
   jmax=-1;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   jmean=0.;      rcurr_time = time(NULL);  
   for(i=1; i<=imx; i++){    for (*iter=1;;++(*iter)) { 
     mi=0;      fp=(*fret); 
     m=firstpass;      ibig=0; 
     while(s[m][i] <= nlstate){      del=0.0; 
       if(s[m][i]>=1)      rlast_time=rcurr_time;
         mw[++mi][i]=m;      /* (void) gettimeofday(&curr_time,&tzp); */
       if(m >=lastpass)      rcurr_time = time(NULL);  
         break;      curr_time = *localtime(&rcurr_time);
       else      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
         m++;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
     }/* end while */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
     if (s[m][i] > nlstate){     for (i=1;i<=n;i++) {
       mi++;     /* Death is another wave */        printf(" %d %.12f",i, p[i]);
       /* if(mi==0)  never been interviewed correctly before death */        fprintf(ficlog," %d %.12lf",i, p[i]);
          /* Only death is a correct wave */        fprintf(ficrespow," %.12lf", p[i]);
       mw[mi][i]=m;      }
     }      printf("\n");
       fprintf(ficlog,"\n");
     wav[i]=mi;      fprintf(ficrespow,"\n");fflush(ficrespow);
     if(mi==0){      if(*iter <=3){
       if(first==0){        tml = *localtime(&rcurr_time);
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);        strcpy(strcurr,asctime(&tml));
         first=1;        rforecast_time=rcurr_time; 
       }        itmp = strlen(strcurr);
       if(first==1){        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);          strcurr[itmp-1]='\0';
       }        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
     } /* end mi==0 */        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){
           rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
   for(i=1; i<=imx; i++){          forecast_time = *localtime(&rforecast_time);
     for(mi=1; mi<wav[i];mi++){          strcpy(strfor,asctime(&forecast_time));
       if (stepm <=0)          itmp = strlen(strfor);
         dh[mi][i]=1;          if(strfor[itmp-1]=='\n')
       else{          strfor[itmp-1]='\0';
         if (s[mw[mi+1][i]][i] > nlstate) {          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 (agedc[i] < 2*AGESUP) {          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);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        }
           if(j==0) j=1;  /* Survives at least one month after exam */      }
           k=k+1;      for (i=1;i<=n;i++) { 
           if (j >= jmax) jmax=j;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           if (j <= jmin) jmin=j;        fptt=(*fret); 
           sum=sum+j;  #ifdef DEBUG
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           }            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
         }  #endif
         else{        printf("%d",i);fflush(stdout);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        fprintf(ficlog,"%d",i);fflush(ficlog);
           k=k+1;        linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
           if (j >= jmax) jmax=j;        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
           else if (j <= jmin)jmin=j;                                         because that direction will be replaced unless the gain del is small
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */                                        in comparison with the 'probable' gain, mu^2, with the last average direction.
           sum=sum+j;                                        Unless the n directions are conjugate some gain in the determinant may be obtained
         }                                        with the new direction.
         jk= j/stepm;                                        */
         jl= j -jk*stepm;          del=fabs(fptt-(*fret)); 
         ju= j -(jk+1)*stepm;          ibig=i; 
         if(jl <= -ju)        } 
           dh[mi][i]=jk;  #ifdef DEBUG
         else        printf("%d %.12e",i,(*fret));
           dh[mi][i]=jk+1;        fprintf(ficlog,"%d %.12e",i,(*fret));
         if(dh[mi][i]==0)        for (j=1;j<=n;j++) {
           dh[mi][i]=1; /* At least one step */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       }          printf(" x(%d)=%.12e",j,xit[j]);
     }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   }        }
   jmean=sum/k;        for(j=1;j<=n;j++) {
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          printf(" p(%d)=%.12e",j,p[j]);
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
  }        }
         printf("\n");
 /*********** Tricode ****************************/        fprintf(ficlog,"\n");
 void tricode(int *Tvar, int **nbcode, int imx)  #endif
 {      } /* end i */
   int Ndum[20],ij=1, k, j, i;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
   int cptcode=0;  #ifdef DEBUG
   cptcoveff=0;        int k[2],l;
          k[0]=1;
   for (k=0; k<19; k++) Ndum[k]=0;        k[1]=-1;
   for (k=1; k<=7; k++) ncodemax[k]=0;        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        for (j=1;j<=n;j++) {
     for (i=1; i<=imx; i++) {          printf(" %.12e",p[j]);
       ij=(int)(covar[Tvar[j]][i]);          fprintf(ficlog," %.12e",p[j]);
       Ndum[ij]++;        }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        printf("\n");
       if (ij > cptcode) cptcode=ij;        fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
     for (i=0; i<=cptcode; i++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       if(Ndum[i]!=0) ncodemax[j]++;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     ij=1;          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (i=1; i<=ncodemax[j]; i++) {        }
       for (k=0; k<=19; k++) {  #endif
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;  
                  free_vector(xit,1,n); 
           ij++;        free_vector(xits,1,n); 
         }        free_vector(ptt,1,n); 
         if (ij > ncodemax[j]) break;        free_vector(pt,1,n); 
       }          return; 
     }      } 
   }        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) */
  for (k=0; k<19; k++) Ndum[k]=0;        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
  for (i=1; i<=ncovmodel-2; i++) {        pt[j]=p[j]; 
    ij=Tvar[i];      } 
    Ndum[ij]++;      fptt=(*func)(ptt); /* f_3 */
  }      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
         /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
  ij=1;        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
  for (i=1; i<=10; i++) {        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
    if((Ndum[i]!=0) && (i<=ncovcol)){        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
      Tvaraff[ij]=i;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
      ij++;        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
    }        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
  }  #ifdef NRCORIGINAL
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
  cptcoveff=ij-1;  #else
 }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
         t= t- del*SQR(fp-fptt);
 /*********** Health Expectancies ****************/  #endif
         directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
 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 )  #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);
 {        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);
   /* Health expectancies */        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   double age, agelim, hf;        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   double ***p3mat,***varhe;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   double **dnewm,**doldm;        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 *xp;        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 **gp, **gm;  #endif
   double ***gradg, ***trgradg;  #ifdef POWELLORIGINAL
   int theta;        if (t < 0.0) { /* Then we use it for new direction */
   #else
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        if (directest*t < 0.0) { /* Contradiction between both tests */
   xp=vector(1,npar);        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
   dnewm=matrix(1,nlstate*2,1,npar);        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   doldm=matrix(1,nlstate*2,1,nlstate*2);        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   fprintf(ficreseij,"# Health expectancies\n");      } 
   fprintf(ficreseij,"# Age");        if (directest < 0.0) { /* Then we use it for new direction */
   for(i=1; i<=nlstate;i++)  #endif
     for(j=1; j<=nlstate;j++)          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          for (j=1;j<=n;j++) { 
   fprintf(ficreseij,"\n");            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
             xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
   if(estepm < stepm){          }
     printf ("Problem %d lower than %d\n",estepm, stepm);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   }          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   else  hstepm=estepm;    
   /* We compute the life expectancy from trapezoids spaced every estepm months  #ifdef DEBUG
    * This is mainly to measure the difference between two models: for example          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
    * if stepm=24 months pijx are given only every 2 years and by summing them          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
    * we are calculating an estimate of the Life Expectancy assuming a linear          for(j=1;j<=n;j++){
    * progression inbetween and thus overestimating or underestimating according            printf(" %.12e",xit[j]);
    * to the curvature of the survival function. If, for the same date, we            fprintf(ficlog," %.12e",xit[j]);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months          }
    * to compare the new estimate of Life expectancy with the same linear          printf("\n");
    * hypothesis. A more precise result, taking into account a more precise          fprintf(ficlog,"\n");
    * curvature will be obtained if estepm is as small as stepm. */  #endif
         } /* end of t negative */
   /* For example we decided to compute the life expectancy with the smallest unit */      } /* end if (fptt < fp)  */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    } 
      nhstepm is the number of hstepm from age to agelim  } 
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size  /**** Prevalence limit (stable or period prevalence)  ****************/
      and note for a fixed period like estepm months */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
      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    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       matrix by transitions matrix until convergence is reached */
      results. So we changed our mind and took the option of the best precision.    
   */    int i, ii,j,k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    double min, max, maxmin, maxmax,sumnew=0.;
     /* double **matprod2(); */ /* test */
   agelim=AGESUP;    double **out, cov[NCOVMAX+1], **pmij();
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double **newm;
     /* nhstepm age range expressed in number of stepm */    double agefin, delaymax=50 ; /* Max number of years to converge */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    for (ii=1;ii<=nlstate+ndeath;ii++)
     /* if (stepm >= YEARM) hstepm=1;*/      for (j=1;j<=nlstate+ndeath;j++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    
     gp=matrix(0,nhstepm,1,nlstate*2);    cov[1]=1.;
     gm=matrix(0,nhstepm,1,nlstate*2);    
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      newm=savm;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        /* Covariates have to be included here again */
        cov[2]=agefin;
       
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      for (k=1; k<=cptcovn;k++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     /* Computing Variances of health expectancies */        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
       }
      for(theta=1; theta <=npar; theta++){      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(i=1; i<=npar; i++){      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
       }      
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       cptj=0;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for(j=1; j<= nlstate; j++){      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         for(i=1; i<=nlstate; i++){      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
           cptj=cptj+1;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      savm=oldm;
           }      oldm=newm;
         }      maxmax=0.;
       }      for(j=1;j<=nlstate;j++){
              min=1.;
              max=0.;
       for(i=1; i<=npar; i++)        for(i=1; i<=nlstate; i++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          sumnew=0;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                prlim[i][j]= newm[i][j]/(1-sumnew);
       cptj=0;          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
       for(j=1; j<= nlstate; j++){          max=FMAX(max,prlim[i][j]);
         for(i=1;i<=nlstate;i++){          min=FMIN(min,prlim[i][j]);
           cptj=cptj+1;        }
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){        maxmin=max-min;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        maxmax=FMAX(maxmax,maxmin);
           }      } /* j loop */
         }      if(maxmax < ftolpl){
       }        return prlim;
       for(j=1; j<= nlstate*2; j++)      }
         for(h=0; h<=nhstepm-1; h++){    } /* age loop */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    return prlim; /* should not reach here */
         }  }
      }  
      /*************** transition probabilities ***************/ 
 /* End theta */  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  {
     /* According to parameters values stored in x and the covariate's values stored in cov,
      for(h=0; h<=nhstepm-1; h++)       computes the probability to be observed in state j being in state i by appying the
       for(j=1; j<=nlstate*2;j++)       model to the ncovmodel covariates (including constant and age).
         for(theta=1; theta <=npar; theta++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
           trgradg[h][j][theta]=gradg[h][theta][j];       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
             ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
      for(i=1;i<=nlstate*2;i++)       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       for(j=1;j<=nlstate*2;j++)       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
         varhe[i][j][(int)age] =0.;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
        Outputs ps[i][j] the probability to be observed in j being in j according to
      printf("%d|",(int)age);fflush(stdout);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    */
      for(h=0;h<=nhstepm-1;h++){    double s1, lnpijopii;
       for(k=0;k<=nhstepm-1;k++){    /*double t34;*/
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    int i,j, nc, ii, jj;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  
         for(i=1;i<=nlstate*2;i++)      for(i=1; i<= nlstate; i++){
           for(j=1;j<=nlstate*2;j++)        for(j=1; j<i;j++){
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       }            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     }            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     /* Computing expectancies */  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     for(i=1; i<=nlstate;i++)          }
       for(j=1; j<=nlstate;j++)          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        }
                  for(j=i+1; j<=nlstate+ndeath;j++){
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
         }            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     fprintf(ficreseij,"%3.0f",age );          }
     cptj=0;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++){      }
         cptj++;      
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      for(i=1; i<= nlstate; i++){
       }        s1=0;
     fprintf(ficreseij,"\n");        for(j=1; j<i; j++){
              s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     free_matrix(gm,0,nhstepm,1,nlstate*2);          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     free_matrix(gp,0,nhstepm,1,nlstate*2);        }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        for(j=i+1; j<=nlstate+ndeath; j++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   }        }
   printf("\n");        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   fprintf(ficlog,"\n");        ps[i][i]=1./(s1+1.);
         /* Computing other pijs */
   free_vector(xp,1,npar);        for(j=1; j<i; j++)
   free_matrix(dnewm,1,nlstate*2,1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        for(j=i+1; j<=nlstate+ndeath; j++)
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          ps[i][j]= exp(ps[i][j])*ps[i][i];
 }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
 /************ Variance ******************/      
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 {        for(jj=1; jj<= nlstate+ndeath; jj++){
   /* Variance of health expectancies */          ps[ii][jj]=0;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          ps[ii][ii]=1;
   /* double **newm;*/        }
   double **dnewm,**doldm;      }
   double **dnewmp,**doldmp;      
   int i, j, nhstepm, hstepm, h, nstepm ;      
   int k, cptcode;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   double *xp;      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   double **gp, **gm;  /* for var eij */      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   double ***gradg, ***trgradg; /*for var eij */      /*   } */
   double **gradgp, **trgradgp; /* for var p point j */      /*   printf("\n "); */
   double *gpp, *gmp; /* for var p point j */      /* } */
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */      /* printf("\n ");printf("%lf ",cov[2]);*/
   double ***p3mat;      /*
   double age,agelim, hf;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   int theta;        goto end;*/
   char digit[4];      return ps;
   char digitp[16];  }
   
   char fileresprobmorprev[FILENAMELENGTH];  /**************** Product of 2 matrices ******************/
   
   if(popbased==1)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
     strcpy(digitp,"-populbased-");  {
   else    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     strcpy(digitp,"-stablbased-");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
   strcpy(fileresprobmorprev,"prmorprev");       before: only the contents of out is modified. The function returns
   sprintf(digit,"%-d",ij);       a pointer to pointers identical to out */
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    int i, j, k;
   strcat(fileresprobmorprev,digit); /* Tvar to be done */    for(i=nrl; i<= nrh; i++)
   strcat(fileresprobmorprev,digitp); /* Popbased or not */      for(k=ncolol; k<=ncoloh; k++){
   strcat(fileresprobmorprev,fileres);        out[i][k]=0.;
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {        for(j=ncl; j<=nch; j++)
     printf("Problem with resultfile: %s\n", fileresprobmorprev);          out[i][k] +=in[i][j]*b[j][k];
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      }
   }    return out;
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);  }
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);  
   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);  /************* Higher Matrix Product ***************/
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){  
     fprintf(ficresprobmorprev," p.%-d SE",j);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for(i=1; i<=nlstate;i++)  {
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);    /* Computes the transition matrix starting at age 'age' over 
   }         'nhstepm*hstepm*stepm' months (i.e. until
   fprintf(ficresprobmorprev,"\n");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {       nhstepm*hstepm matrices. 
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);       (typically every 2 years instead of every month which is too big 
     exit(0);       for the memory).
   }       Model is determined by parameters x and covariates have to be 
   else{       included manually here. 
     fprintf(ficgp,"\n# Routine varevsij");  
   }       */
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  
     printf("Problem with html file: %s\n", optionfilehtm);    int i, j, d, h, k;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    double **out, cov[NCOVMAX+1];
     exit(0);    double **newm;
   }  
   else{    /* Hstepm could be zero and should return the unit matrix */
     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");    for (i=1;i<=nlstate+ndeath;i++)
   }      for (j=1;j<=nlstate+ndeath;j++){
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
   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");      }
   fprintf(ficresvij,"# Age");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(i=1; i<=nlstate;i++)    for(h=1; h <=nhstepm; h++){
     for(j=1; j<=nlstate;j++)      for(d=1; d <=hstepm; d++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        newm=savm;
   fprintf(ficresvij,"\n");        /* Covariates have to be included here again */
         cov[1]=1.;
   xp=vector(1,npar);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   dnewm=matrix(1,nlstate,1,npar);        for (k=1; k<=cptcovn;k++) 
   doldm=matrix(1,nlstate,1,nlstate);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);        for (k=1; k<=cptcovage;k++)
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   gpp=vector(nlstate+1,nlstate+ndeath);  
   gmp=vector(nlstate+1,nlstate+ndeath);  
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
          /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   if(estepm < stepm){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     printf ("Problem %d lower than %d\n",estepm, stepm);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   }        savm=oldm;
   else  hstepm=estepm;          oldm=newm;
   /* 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.      for(i=1; i<=nlstate+ndeath; i++)
      nhstepm is the number of hstepm from age to agelim        for(j=1;j<=nlstate+ndeath;j++) {
      nstepm is the number of stepm from age to agelin.          po[i][j][h]=newm[i][j];
      Look at hpijx to understand the reason of that which relies in memory size          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
      and note for a fixed period like k years */        }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      /*printf("h=%d ",h);*/
      survival function given by stepm (the optimization length). Unfortunately it    } /* end h */
      means that if the survival funtion is printed only each two years of age and if  /*     printf("\n H=%d \n",h); */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    return po;
      results. So we changed our mind and took the option of the best precision.  }
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  #ifdef NLOPT
   agelim = AGESUP;    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double fret;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double *xt;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    int j;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    myfunc_data *d2 = (myfunc_data *) pd;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  /* xt = (p1-1); */
     gp=matrix(0,nhstepm,1,nlstate);    xt=vector(1,n); 
     gm=matrix(0,nhstepm,1,nlstate);    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   
     fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     for(theta=1; theta <=npar; theta++){    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
       for(i=1; i<=npar; i++){ /* Computes gradient */    printf("Function = %.12lf ",fret);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
       }    printf("\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     free_vector(xt,1,n);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return fret;
   }
       if (popbased==1) {  #endif
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  /*************** log-likelihood *************/
       }  double func( double *x)
    {
       for(j=1; j<= nlstate; j++){    int i, ii, j, k, mi, d, kk;
         for(h=0; h<=nhstepm; h++){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double **out;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    double sw; /* Sum of weights */
         }    double lli; /* Individual log likelihood */
       }    int s1, s2;
       /* This for computing forces of mortality (h=1)as a weighted average */    double bbh, survp;
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    long ipmx;
         for(i=1; i<= nlstate; i++)    /*extern weight */
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    /* We are differentiating ll according to initial status */
       }        /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       /* end force of mortality */    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
       for(i=1; i<=npar; i++) /* Computes gradient */    */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      ++countcallfunc;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
      cov[1]=1.;
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
           prlim[i][i]=probs[(int)age][i][ij];  
       }    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(j=1; j<= nlstate; j++){        /* Computes the values of the ncovmodel covariates of the model
         for(h=0; h<=nhstepm; h++){           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];           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 */
       /* This for computing force of mortality (h=1)as a weighted average */          cov[2+k]=covar[Tvar[k]][i];
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){        }
         for(i=1; i<= nlstate; i++)        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
           gmp[j] += prlim[i][i]*p3mat[i][j][1];           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       }               has been calculated etc */
       /* end force of mortality */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<= nlstate; j++) /* vareij */            for (j=1;j<=nlstate+ndeath;j++){
         for(h=0; h<=nhstepm; h++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          for(d=0; d<dh[mi][i]; d++){
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     } /* End theta */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
             }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(h=0; h<=nhstepm; h++) /* veij */            savm=oldm;
       for(j=1; j<=nlstate;j++)            oldm=newm;
         for(theta=1; theta <=npar; theta++)          } /* end mult */
           trgradg[h][j][theta]=gradg[h][theta][j];        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */          /* But now since version 0.9 we anticipate for bias at large stepm.
       for(theta=1; theta <=npar; theta++)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         trgradgp[j][theta]=gradgp[theta][j];           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for(i=1;i<=nlstate;i++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       for(j=1;j<=nlstate;j++)           * probability in order to take into account the bias as a fraction of the way
         vareij[i][j][(int)age] =0.;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
     for(h=0;h<=nhstepm;h++){           * For stepm=1 the results are the same as for previous versions of Imach.
       for(k=0;k<=nhstepm;k++){           * For stepm > 1 the results are less biased than in previous versions. 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);           */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          s1=s[mw[mi][i]][i];
         for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
           for(j=1;j<=nlstate;j++)          bbh=(double)bh[mi][i]/(double)stepm; 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          /* bias bh is positive if real duration
       }           * is higher than the multiple of stepm and negative otherwise.
     }           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     /* pptj */          if( s2 > nlstate){ 
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);            /* i.e. if s2 is a death state and if the date of death is known 
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);               then the contribution to the likelihood is the probability to 
     for(j=nlstate+1;j<=nlstate+ndeath;j++)               die between last step unit time and current  step unit time, 
       for(i=nlstate+1;i<=nlstate+ndeath;i++)               which is also equal to probability to die before dh 
         varppt[j][i]=doldmp[j][i];               minus probability to die before dh-stepm . 
     /* end ppptj */               In version up to 0.92 likelihood was computed
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);            as if date of death was unknown. Death was treated as any other
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);          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
     if (popbased==1) {          to consider that at each interview the state was recorded
       for(i=1; i<=nlstate;i++)          (healthy, disable or death) and IMaCh was corrected; but when we
         prlim[i][i]=probs[(int)age][i][ij];          introduced the exact date of death then we should have modified
     }          the contribution of an exact death to the likelihood. This new
              contribution is smaller and very dependent of the step unit
     /* This for computing force of mortality (h=1)as a weighted average */          stepm. It is no more the probability to die between last interview
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          and month of death but the probability to survive from last
       for(i=1; i<= nlstate; i++)          interview up to one month before death multiplied by the
         gmp[j] += prlim[i][i]*p3mat[i][j][1];          probability to die within a month. Thanks to Chris
     }              Jackson for correcting this bug.  Former versions increased
     /* end force of mortality */          mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);          lower mortality.
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){            */
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));          /* If, at the beginning of the maximization mostly, the
       for(i=1; i<=nlstate;i++){             cumulative probability or probability to be dead is
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);             constant (ie = 1) over time d, the difference is equal to
       }             0.  out[s1][3] = savm[s1][3]: probability, being at state
     }             s1 at precedent wave, to be dead a month before current
     fprintf(ficresprobmorprev,"\n");             wave is equal to probability, being at state s1 at
              precedent wave, to be dead at mont of the current
     fprintf(ficresvij,"%.0f ",age );             wave. Then the observed probability (that this person died)
     for(i=1; i<=nlstate;i++)             is null according to current estimated parameter. In fact,
       for(j=1; j<=nlstate;j++){             it should be very low but not zero otherwise the log go to
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);             infinity.
       }          */
     fprintf(ficresvij,"\n");  /* #ifdef INFINITYORIGINAL */
     free_matrix(gp,0,nhstepm,1,nlstate);  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
     free_matrix(gm,0,nhstepm,1,nlstate);  /* #else */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  /*          lli=log(mytinydouble); */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*        else */
   } /* End age */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   free_vector(gpp,nlstate+1,nlstate+ndeath);  /* #endif */
   free_vector(gmp,nlstate+1,nlstate+ndeath);              lli=log(out[s1][s2] - savm[s1][s2]);
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);  
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/          } else if  (s2==-2) {
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");            for (j=1,survp=0. ; j<=nlstate; j++) 
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");            /*survp += out[s1][j]; */
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);            lli= log(survp);
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);          }
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);          
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);          else if  (s2==-4) { 
   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);            for (j=3,survp=0. ; j<=nlstate; j++)  
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
   free_vector(xp,1,npar);          } 
   free_matrix(doldm,1,nlstate,1,nlstate);  
   free_matrix(dnewm,1,nlstate,1,npar);          else if  (s2==-5) { 
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            for (j=1,survp=0. ; j<=2; j++)  
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            lli= log(survp); 
   fclose(ficresprobmorprev);          } 
   fclose(ficgp);          
   fclose(fichtm);          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
 /************ Variance of prevlim ******************/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 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)          /*if(lli ==000.0)*/
 {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   /* Variance of prevalence limit */          ipmx +=1;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          sw += weight[i];
   double **newm;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **dnewm,**doldm;          /* if (lli < log(mytinydouble)){ */
   int i, j, nhstepm, hstepm;          /*   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); */
   int k, cptcode;          /*   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]); */
   double *xp;          /* } */
   double *gp, *gm;        } /* end of wave */
   double **gradg, **trgradg;      } /* end of individual */
   double age,agelim;    }  else if(mle==2){
   int theta;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
            for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");        for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficresvpl,"# Age");          for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficresvpl," %1d-%1d",i,i);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   xp=vector(1,npar);          for(d=0; d<=dh[mi][i]; d++){
   dnewm=matrix(1,nlstate,1,npar);            newm=savm;
   doldm=matrix(1,nlstate,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
   hstepm=1*YEARM; /* Every year of age */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            }
   agelim = AGESUP;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            savm=oldm;
     if (stepm >= YEARM) hstepm=1;            oldm=newm;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          } /* end mult */
     gradg=matrix(1,npar,1,nlstate);        
     gp=vector(1,nlstate);          s1=s[mw[mi][i]][i];
     gm=vector(1,nlstate);          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
     for(theta=1; theta <=npar; theta++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       for(i=1; i<=npar; i++){ /* Computes gradient */          ipmx +=1;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* end of wave */
       for(i=1;i<=nlstate;i++)      } /* end of individual */
         gp[i] = prlim[i][i];    }  else if(mle==3){  /* exponential inter-extrapolation */
          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(i=1; i<=npar; i++) /* Computes gradient */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(mi=1; mi<= wav[i]-1; mi++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1;i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
         gm[i] = prlim[i][i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1;i<=nlstate;i++)            }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          for(d=0; d<dh[mi][i]; d++){
     } /* End theta */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     trgradg =matrix(1,nlstate,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(j=1; j<=nlstate;j++)            }
       for(theta=1; theta <=npar; theta++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         trgradg[j][theta]=gradg[theta][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(i=1;i<=nlstate;i++)            oldm=newm;
       varpl[i][(int)age] =0.;          } /* end mult */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          s1=s[mw[mi][i]][i];
     for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     fprintf(ficresvpl,"%.0f ",age );          ipmx +=1;
     for(i=1; i<=nlstate;i++)          sw += weight[i];
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     fprintf(ficresvpl,"\n");        } /* end of wave */
     free_vector(gp,1,nlstate);      } /* end of individual */
     free_vector(gm,1,nlstate);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     free_matrix(gradg,1,npar,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_matrix(trgradg,1,nlstate,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   } /* End age */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   free_vector(xp,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(doldm,1,nlstate,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(dnewm,1,nlstate,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 /************ Variance of one-step probabilities  ******************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)            for (kk=1; kk<=cptcovage;kk++) {
 {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, j=0,  i1, k1, l1, t, tj;            }
   int k2, l2, j1,  z1;          
   int k=0,l, cptcode;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int first=1, first1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;            savm=oldm;
   double **dnewm,**doldm;            oldm=newm;
   double *xp;          } /* end mult */
   double *gp, *gm;        
   double **gradg, **trgradg;          s1=s[mw[mi][i]][i];
   double **mu;          s2=s[mw[mi+1][i]][i];
   double age,agelim, cov[NCOVMAX];          if( s2 > nlstate){ 
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */            lli=log(out[s1][s2] - savm[s1][s2]);
   int theta;          }else{
   char fileresprob[FILENAMELENGTH];            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   char fileresprobcov[FILENAMELENGTH];          }
   char fileresprobcor[FILENAMELENGTH];          ipmx +=1;
           sw += weight[i];
   double ***varpij;          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]); */
   strcpy(fileresprob,"prob");        } /* end of wave */
   strcat(fileresprob,fileres);      } /* end of individual */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     printf("Problem with resultfile: %s\n", fileresprob);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   strcpy(fileresprobcov,"probcov");          for (ii=1;ii<=nlstate+ndeath;ii++)
   strcat(fileresprobcov,fileres);            for (j=1;j<=nlstate+ndeath;j++){
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("Problem with resultfile: %s\n", fileresprobcov);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);            }
   }          for(d=0; d<dh[mi][i]; d++){
   strcpy(fileresprobcor,"probcor");            newm=savm;
   strcat(fileresprobcor,fileres);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {            for (kk=1; kk<=cptcovage;kk++) {
     printf("Problem with resultfile: %s\n", fileresprobcor);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);            }
   }          
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);            savm=oldm;
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);            oldm=newm;
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);          } /* end mult */
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);        
            s1=s[mw[mi][i]][i];
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");          s2=s[mw[mi+1][i]][i];
   fprintf(ficresprob,"# Age");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");          ipmx +=1;
   fprintf(ficresprobcov,"# Age");          sw += weight[i];
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficresprobcov,"# Age");          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
       } /* end of individual */
   for(i=1; i<=nlstate;i++)    } /* End of if */
     for(j=1; j<=(nlstate+ndeath);j++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    return -l;
     }    }
   fprintf(ficresprob,"\n");  
   fprintf(ficresprobcov,"\n");  /*************** log-likelihood *************/
   fprintf(ficresprobcor,"\n");  double funcone( double *x)
   xp=vector(1,npar);  {
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    /* Same as likeli but slower because of a lot of printf and if */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    int i, ii, j, k, mi, d, kk;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    double **out;
   first=1;    double lli; /* Individual log likelihood */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    double llt;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    int s1, s2;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    double bbh, survp;
     exit(0);    /*extern weight */
   }    /* We are differentiating ll according to initial status */
   else{    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     fprintf(ficgp,"\n# Routine varprob");    /*for(i=1;i<imx;i++) 
   }      printf(" %d\n",s[4][i]);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    */
     printf("Problem with html file: %s\n", optionfilehtm);    cov[1]=1.;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);  
     exit(0);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   }  
   else{    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(fichtm,"\n");      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");          for (j=1;j<=nlstate+ndeath;j++){
     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");            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     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");            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   }        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   cov[1]=1;          for (kk=1; kk<=cptcovage;kk++) {
   tj=cptcoveff;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}          }
   j1=0;          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   for(t=1; t<=tj;t++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i1=1; i1<=ncodemax[t];i1++){                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       j1++;          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
                /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
       if  (cptcovn>0) {          savm=oldm;
         fprintf(ficresprob, "\n#********** Variable ");          oldm=newm;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        } /* end mult */
         fprintf(ficresprob, "**********\n#");        
         fprintf(ficresprobcov, "\n#********** Variable ");        s1=s[mw[mi][i]][i];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        s2=s[mw[mi+1][i]][i];
         fprintf(ficresprobcov, "**********\n#");        bbh=(double)bh[mi][i]/(double)stepm; 
                /* bias is positive if real duration
         fprintf(ficgp, "\n#********** Variable ");         * is higher than the multiple of stepm and negative otherwise.
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);         */
         fprintf(ficgp, "**********\n#");        if( s2 > nlstate && (mle <5) ){  /* Jackson */
                  lli=log(out[s1][s2] - savm[s1][s2]);
                } else if  (s2==-2) {
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          for (j=1,survp=0. ; j<=nlstate; j++) 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");          lli= log(survp);
                }else if (mle==1){
         fprintf(ficresprobcor, "\n#********** Variable ");              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        } else if(mle==2){
         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 */
       }        } else if(mle==3){  /* exponential inter-extrapolation */
                lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       for (age=bage; age<=fage; age ++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         cov[2]=age;          lli=log(out[s1][s2]); /* Original formula */
         for (k=1; k<=cptcovn;k++) {        } else{  /* mle=0 back to 1 */
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         }          /*lli=log(out[s1][s2]); */ /* Original formula */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        } /* End of if */
         for (k=1; k<=cptcovprod;k++)        ipmx +=1;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        sw += weight[i];
                ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));        /*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]); */
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        if(globpr){
         gp=vector(1,(nlstate)*(nlstate+ndeath));          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
         gm=vector(1,(nlstate)*(nlstate+ndeath));   %11.6f %11.6f %11.6f ", \
                      num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         for(theta=1; theta <=npar; theta++){                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(i=1; i<=npar; i++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             xp[i] = x[i] + (i==theta ?delti[theta]:0);            llt +=ll[k]*gipmx/gsw;
                      fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          }
                    fprintf(ficresilk," %10.6f\n", -llt);
           k=0;        }
           for(i=1; i<= (nlstate); i++){      } /* end of wave */
             for(j=1; j<=(nlstate+ndeath);j++){    } /* end of individual */
               k=k+1;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
               gp[k]=pmmij[i][j];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
             }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           }    if(globpr==0){ /* First time we count the contributions and weights */
                gipmx=ipmx;
           for(i=1; i<=npar; i++)      gsw=sw;
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    }
        return -l;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  }
           k=0;  
           for(i=1; i<=(nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){  /*************** function likelione ***********/
               k=k+1;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
               gm[k]=pmmij[i][j];  {
             }    /* This routine should help understanding what is done with 
           }       the selection of individuals/waves and
             to check the exact contribution to the likelihood.
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)       Plotting could be done.
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];       */
         }    int k;
   
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    if(*globpri !=0){ /* Just counts and sums, no printings */
           for(theta=1; theta <=npar; theta++)      strcpy(fileresilk,"ilk"); 
             trgradg[j][theta]=gradg[theta][j];      strcat(fileresilk,fileres);
              if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);        printf("Problem with resultfile: %s\n", fileresilk);
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
              }
         pmij(pmmij,cov,ncovmodel,x,nlstate);      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
              fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         k=0;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         for(i=1; i<=(nlstate); i++){      for(k=1; k<=nlstate; k++) 
           for(j=1; j<=(nlstate+ndeath);j++){        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
             k=k+1;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
             mu[k][(int) age]=pmmij[i][j];    }
           }  
         }    *fretone=(*funcone)(p);
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    if(*globpri !=0){
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)      fclose(ficresilk);
             varpij[i][j][(int)age] = doldm[i][j];      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
         /*printf("\n%d ",(int)age);    } 
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    return;
        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]));  
      }*/  
   /*********** Maximum Likelihood Estimation ***************/
         fprintf(ficresprob,"\n%d ",(int)age);  
         fprintf(ficresprobcov,"\n%d ",(int)age);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         fprintf(ficresprobcor,"\n%d ",(int)age);  {
     int i,j, iter=0;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    double **xi;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    double fret;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    double fretone; /* Only one call to likelihood */
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    /*  char filerespow[FILENAMELENGTH];*/
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  
         }  #ifdef NLOPT
         i=0;    int creturn;
         for (k=1; k<=(nlstate);k++){    nlopt_opt opt;
           for (l=1; l<=(nlstate+ndeath);l++){    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
             i=i++;    double *lb;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    double minf; /* the minimum objective value, upon return */
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    double * p1; /* Shifted parameters from 0 instead of 1 */
             for (j=1; j<=i;j++){    myfunc_data dinst, *d = &dinst;
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);  #endif
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));  
             }  
           }    xi=matrix(1,npar,1,npar);
         }/* end of loop for state */    for (i=1;i<=npar;i++)
       } /* end of loop for age */      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
       /* Confidence intervalle of pij  */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       /*    strcpy(filerespow,"pow"); 
       fprintf(ficgp,"\nset noparametric;unset label");    strcat(filerespow,fileres);
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");      printf("Problem with resultfile: %s\n", filerespow);
       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(ficlog,"Problem with resultfile: %s\n", filerespow);
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);    }
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);    for (i=1;i<=nlstate;i++)
       */      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    fprintf(ficrespow,"\n");
       first1=1;  #ifdef POWELL
       for (k1=1; k1<=(nlstate);k1++){    powell(p,xi,npar,ftol,&iter,&fret,func);
         for (l1=1; l1<=(nlstate+ndeath);l1++){  #endif
           if(l1==k1) continue;  
           i=(k1-1)*(nlstate+ndeath)+l1;  #ifdef NLOPT
           for (k2=1; k2<=(nlstate);k2++){  #ifdef NEWUOA
             for (l2=1; l2<=(nlstate+ndeath);l2++){    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
               if(l2==k2) continue;  #else
               j=(k2-1)*(nlstate+ndeath)+l2;    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
               if(j<=i) continue;  #endif
               for (age=bage; age<=fage; age ++){    lb=vector(0,npar-1);
                 if ((int)age %5==0){    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    nlopt_set_lower_bounds(opt, lb);
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    nlopt_set_initial_step1(opt, 0.1);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    
                   mu1=mu[i][(int) age]/stepm*YEARM ;    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
                   mu2=mu[j][(int) age]/stepm*YEARM;    d->function = func;
                   /* Computing eigen value of matrix of covariance */    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    nlopt_set_min_objective(opt, myfunc, d);
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    nlopt_set_xtol_rel(opt, ftol);
                   if(first1==1){    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
                     first1=0;      printf("nlopt failed! %d\n",creturn); 
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);    }
                   }    else {
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
                   /* Eigen vectors */      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));      iter=1; /* not equal */
                   v21=sqrt(1.-v11*v11);    }
                   v12=-v21;    nlopt_destroy(opt);
                   v22=v11;  #endif
                   /*printf(fignu*/    free_matrix(xi,1,npar,1,npar);
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    fclose(ficrespow);
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                   if(first==1){    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                     first=0;    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                     fprintf(ficgp,"\nset parametric;set nolabel");  
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);  }
                     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>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);  /**** Computes Hessian and covariance matrix ***/
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);  {
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    double  **a,**y,*x,pd;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    double **hess;
                     /*              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)) t \"%d\"",\    int i, j;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    int *indx;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  
                     */    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
                     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 hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    void lubksb(double **a, int npar, int *indx, double b[]) ;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));    void ludcmp(double **a, int npar, int *indx, double *d) ;
                   }else{    double gompertz(double p[]);
                     first=0;    hess=matrix(1,npar,1,npar);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    printf("\nCalculation of the hessian matrix. Wait...\n");
                     /*    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                     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)) t \"%d\"",\    for (i=1;i<=npar;i++){
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      printf("%d",i);fflush(stdout);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      fprintf(ficlog,"%d",i);fflush(ficlog);
                     */     
                     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",\       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));      /*  printf(" %f ",p[i]);
                   }/* if first */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
                 } /* age mod 5 */    }
               } /* end loop age */    
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);    for (i=1;i<=npar;i++) {
               first=1;      for (j=1;j<=npar;j++)  {
             } /*l12 */        if (j>i) { 
           } /* k12 */          printf(".%d%d",i,j);fflush(stdout);
         } /*l1 */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       }/* k1 */          hess[i][j]=hessij(p,delti,i,j,func,npar);
     } /* loop covariates */          
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);          hess[j][i]=hess[i][j];    
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          /*printf(" %lf ",hess[i][j]);*/
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        }
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);      }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    printf("\n");
   }    fprintf(ficlog,"\n");
   free_vector(xp,1,npar);  
   fclose(ficresprob);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   fclose(ficresprobcov);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   fclose(ficresprobcor);    
   fclose(ficgp);    a=matrix(1,npar,1,npar);
   fclose(fichtm);    y=matrix(1,npar,1,npar);
 }    x=vector(1,npar);
     indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
 /******************* Printing html file ***********/      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    ludcmp(a,npar,indx,&pd);
                   int lastpass, int stepm, int weightopt, char model[],\  
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    for (j=1;j<=npar;j++) {
                   int popforecast, int estepm ,\      for (i=1;i<=npar;i++) x[i]=0;
                   double jprev1, double mprev1,double anprev1, \      x[j]=1;
                   double jprev2, double mprev2,double anprev2){      lubksb(a,npar,indx,x);
   int jj1, k1, i1, cpt;      for (i=1;i<=npar;i++){ 
   /*char optionfilehtm[FILENAMELENGTH];*/        matcov[i][j]=x[i];
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {      }
     printf("Problem with %s \n",optionfilehtm), exit(0);    }
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);  
   }    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    for (i=1;i<=npar;i++) { 
  - 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      for (j=1;j<=npar;j++) { 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        printf("%.3e ",hess[i][j]);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n        fprintf(ficlog,"%.3e ",hess[i][j]);
  - Life expectancies by age and initial health status (estepm=%2d months):      }
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      printf("\n");
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      fprintf(ficlog,"\n");
     }
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  
     /* Recompute Inverse */
  m=cptcoveff;    for (i=1;i<=npar;i++)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
  jj1=0;  
  for(k1=1; k1<=m;k1++){    /*  printf("\n#Hessian matrix recomputed#\n");
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;    for (j=1;j<=npar;j++) {
      if (cptcovn > 0) {      for (i=1;i<=npar;i++) x[i]=0;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      x[j]=1;
        for (cpt=1; cpt<=cptcoveff;cpt++)      lubksb(a,npar,indx,x);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      for (i=1;i<=npar;i++){ 
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        y[i][j]=x[i];
      }        printf("%.3e ",y[i][j]);
      /* Pij */        fprintf(ficlog,"%.3e ",y[i][j]);
      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>      }
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          printf("\n");
      /* Quasi-incidences */      fprintf(ficlog,"\n");
      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>    }
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    */
        /* Stable prevalence in each health state */  
        for(cpt=1; cpt<nlstate;cpt++){    free_matrix(a,1,npar,1,npar);
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    free_matrix(y,1,npar,1,npar);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    free_vector(x,1,npar);
        }    free_ivector(indx,1,npar);
      for(cpt=1; cpt<=nlstate;cpt++) {    free_matrix(hess,1,npar,1,npar);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>  
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }  }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.png<br>  /*************** hessian matrix ****************/
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
    } /* end i1 */  {
  }/* End k1 */    int i;
  fprintf(fichtm,"</ul>");    int l=1, lmax=20;
     double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    double res;
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    double fx;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    int k=0,kmax=10;
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    double l1;
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    fx=func(x);
  - 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);    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
  if(popforecast==1) fprintf(fichtm,"\n      l1=pow(10,l);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      delts=delt;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      for(k=1 ; k <kmax; k=k+1){
         <br>",fileres,fileres,fileres,fileres);        delt = delta*(l1*k);
  else        p2[theta]=x[theta] +delt;
    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);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
  m=cptcoveff;        /*res= (k1-2.0*fx+k2)/delt/delt; */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
  jj1=0;  #ifdef DEBUGHESS
  for(k1=1; k1<=m;k1++){        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);
    for(i1=1; i1<=ncodemax[k1];i1++){        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);
      jj1++;  #endif
      if (cptcovn > 0) {        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
        for (cpt=1; cpt<=cptcoveff;cpt++)          k=kmax;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      }          k=kmax; l=lmax*10;
      for(cpt=1; cpt<=nlstate;cpt++) {        }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 interval) in state (%d): v%s%d%d.png <br>          delts=delt;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }
      }      }
    } /* end i1 */    }
  }/* End k1 */    delti[theta]=delts;
  fprintf(fichtm,"</ul>");    return res; 
 fclose(fichtm);    
 }  }
   
 /******************* Gnuplot file **************/  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  {
     int i;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int l=1, lmax=20;
   int ng;    double k1,k2,k3,k4,res,fx;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    double p2[MAXPARM+1];
     printf("Problem with file %s",optionfilegnuplot);    int k;
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);  
   }    fx=func(x);
     for (k=1; k<=2; k++) {
 #ifdef windows      for (i=1;i<=npar;i++) p2[i]=x[i];
     fprintf(ficgp,"cd \"%s\" \n",pathc);      p2[thetai]=x[thetai]+delti[thetai]/k;
 #endif      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 m=pow(2,cptcoveff);      k1=func(p2)-fx;
      
  /* 1eme*/      p2[thetai]=x[thetai]+delti[thetai]/k;
   for (cpt=1; cpt<= nlstate ; cpt ++) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
    for (k1=1; k1<= m ; k1 ++) {      k2=func(p2)-fx;
     
 #ifdef windows      p2[thetai]=x[thetai]-delti[thetai]/k;
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      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);      k3=func(p2)-fx;
 #endif    
 #ifdef unix      p2[thetai]=x[thetai]-delti[thetai]/k;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      k4=func(p2)-fx;
 #endif      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
 for (i=1; i<= nlstate ; i ++) {      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      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);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  #endif
 }    }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    return res;
     for (i=1; i<= nlstate ; i ++) {  }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  /************** Inverse of matrix **************/
 }  void ludcmp(double **a, int n, int *indx, double *d) 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  { 
      for (i=1; i<= nlstate ; i ++) {    int i,imax,j,k; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double big,dum,sum,temp; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *vv; 
 }     
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    vv=vector(1,n); 
 #ifdef unix    *d=1.0; 
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    for (i=1;i<=n;i++) { 
 #endif      big=0.0; 
    }      for (j=1;j<=n;j++) 
   }        if ((temp=fabs(a[i][j])) > big) big=temp; 
   /*2 eme*/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
   for (k1=1; k1<= m ; k1 ++) {    } 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    for (j=1;j<=n;j++) { 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      for (i=1;i<j;i++) { 
            sum=a[i][j]; 
     for (i=1; i<= nlstate+1 ; i ++) {        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       k=2*i;        a[i][j]=sum; 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      } 
       for (j=1; j<= nlstate+1 ; j ++) {      big=0.0; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for (i=j;i<=n;i++) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        sum=a[i][j]; 
 }          for (k=1;k<j;k++) 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          sum -= a[i][k]*a[k][j]; 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        a[i][j]=sum; 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       for (j=1; j<= nlstate+1 ; j ++) {          big=dum; 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          imax=i; 
         else fprintf(ficgp," \%%*lf (\%%*lf)");        } 
 }        } 
       fprintf(ficgp,"\" t\"\" w l 0,");      if (j != imax) { 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        for (k=1;k<=n;k++) { 
       for (j=1; j<= nlstate+1 ; j ++) {          dum=a[imax][k]; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          a[imax][k]=a[j][k]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          a[j][k]=dum; 
 }          } 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        *d = -(*d); 
       else fprintf(ficgp,"\" t\"\" w l 0,");        vv[imax]=vv[j]; 
     }      } 
   }      indx[j]=imax; 
        if (a[j][j] == 0.0) a[j][j]=TINY; 
   /*3eme*/      if (j != n) { 
         dum=1.0/(a[j][j]); 
   for (k1=1; k1<= m ; k1 ++) {        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     for (cpt=1; cpt<= nlstate ; cpt ++) {      } 
       k=2+nlstate*(2*cpt-2);    } 
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    free_vector(vv,1,n);  /* Doesn't work */
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  ;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  } 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  void lubksb(double **a, int n, int *indx, double b[]) 
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  { 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    int i,ii=0,ip,j; 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    double sum; 
    
 */    for (i=1;i<=n;i++) { 
       for (i=1; i< nlstate ; i ++) {      ip=indx[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);      sum=b[ip]; 
       b[ip]=b[i]; 
       }      if (ii) 
     }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   }      else if (sum) ii=i; 
        b[i]=sum; 
   /* CV preval stat */    } 
     for (k1=1; k1<= m ; k1 ++) {    for (i=n;i>=1;i--) { 
     for (cpt=1; cpt<nlstate ; cpt ++) {      sum=b[i]; 
       k=3;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      b[i]=sum/a[i][i]; 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    } 
   } 
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);  void pstamp(FILE *fichier)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  {
          fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       l=3+(nlstate+ndeath)*cpt;  }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {  /************ Frequencies ********************/
         l=3+(nlstate+ndeath)*cpt;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
         fprintf(ficgp,"+$%d",l+i+1);  {  /* Some frequencies */
       }    
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      int i, m, jk, j1, bool, z1,j;
     }    int first;
   }      double ***freq; /* Frequencies */
      double *pp, **prop;
   /* proba elementaires */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
    for(i=1,jk=1; i <=nlstate; i++){    char fileresp[FILENAMELENGTH];
     for(k=1; k <=(nlstate+ndeath); k++){    
       if (k != i) {    pp=vector(1,nlstate);
         for(j=1; j <=ncovmodel; j++){    prop=matrix(1,nlstate,iagemin,iagemax+3);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    strcpy(fileresp,"p");
           jk++;    strcat(fileresp,fileres);
           fprintf(ficgp,"\n");    if((ficresp=fopen(fileresp,"w"))==NULL) {
         }      printf("Problem with prevalence resultfile: %s\n", fileresp);
       }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     }      exit(0);
    }    }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    j1=0;
      for(jk=1; jk <=m; jk++) {    
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    j=cptcoveff;
        if (ng==2)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");  
        else    first=1;
          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);    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
        i=1;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
        for(k2=1; k2<=nlstate; k2++) {    /*    j1++; */
          k3=i;    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
          for(k=1; k<=(nlstate+ndeath); k++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
            if (k != k2){          scanf("%d", i);*/
              if(ng==2)        for (i=-5; i<=nlstate+ndeath; i++)  
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
              else            for(m=iagemin; m <= iagemax+3; m++)
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              freq[i][jk][m]=0;
              ij=1;        
              for(j=3; j <=ncovmodel; j++) {        for (i=1; i<=nlstate; i++)  
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for(m=iagemin; m <= iagemax+3; m++)
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            prop[i][m]=0;
                  ij++;        
                }        dateintsum=0;
                else        k2cpt=0;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for (i=1; i<=imx; i++) {
              }          bool=1;
              fprintf(ficgp,")/(1");          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                          for (z1=1; z1<=cptcoveff; z1++)       
              for(k1=1; k1 <=nlstate; k1++){                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                ij=1;                bool=0;
                for(j=3; j <=ncovmodel; j++){                /* 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", 
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
                    ij++;                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                  }              } 
                  else          }
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);   
                }          if (bool==1){
                fprintf(ficgp,")");            for(m=firstpass; m<=lastpass; m++){
              }              k2=anint[m][i]+(mint[m][i]/12.);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
              i=i+ncovmodel;                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];
          } /* end k */                if (m<lastpass) {
        } /* end k2 */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
      } /* end jk */                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    } /* end ng */                }
    fclose(ficgp);                
 }  /* end gnuplot */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
                   k2cpt++;
 /*************** Moving average **************/                }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){                /*}*/
             }
   int i, cpt, cptcod;          }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        } /* end i */
       for (i=1; i<=nlstate;i++)         
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           mobaverage[(int)agedeb][i][cptcod]=0.;        pstamp(ficresp);
            if  (cptcovn>0) {
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          fprintf(ficresp, "\n#********** Variable "); 
       for (i=1; i<=nlstate;i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          fprintf(ficresp, "**********\n#");
           for (cpt=0;cpt<=4;cpt++){          fprintf(ficlog, "\n#********** Variable "); 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficlog, "**********\n#");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        }
         }        for(i=1; i<=nlstate;i++) 
       }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     }        fprintf(ficresp, "\n");
            
 }        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
             fprintf(ficlog,"Total");
 /************** Forecasting ******************/          }else{
 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){            if(first==1){
                first=0;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              printf("See log file for details...\n");
   int *popage;            }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            fprintf(ficlog,"Age %d", i);
   double *popeffectif,*popcount;          }
   double ***p3mat;          for(jk=1; jk <=nlstate ; jk++){
   char fileresf[FILENAMELENGTH];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
  agelim=AGESUP;          }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              pos += freq[jk][m][i];
              if(pp[jk]>=1.e-10){
                if(first==1){
   strcpy(fileresf,"f");                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   strcat(fileresf,fileres);              }
   if((ficresf=fopen(fileresf,"w"))==NULL) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     printf("Problem with forecast resultfile: %s\n", fileresf);            }else{
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   printf("Computing forecasting: result on file '%s' \n", fileresf);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);            }
           }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
           for(jk=1; jk <=nlstate ; jk++){
   if (mobilav==1) {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              pp[jk] += freq[jk][m][i];
     movingaverage(agedeb, fage, ageminpar, mobaverage);          }       
   }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   stepsize=(int) (stepm+YEARM-1)/YEARM;            posprop += prop[jk][i];
   if (stepm<=12) stepsize=1;          }
            for(jk=1; jk <=nlstate ; jk++){
   agelim=AGESUP;            if(pos>=1.e-5){
                if(first==1)
   hstepm=1;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   hstepm=hstepm/stepm;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   yp1=modf(dateintmean,&yp);            }else{
   anprojmean=yp;              if(first==1)
   yp2=modf((yp1*12),&yp);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   mprojmean=yp;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   yp1=modf((yp2*30.5),&yp);            }
   jprojmean=yp;            if( i <= iagemax){
   if(jprojmean==0) jprojmean=1;              if(pos>=1.e-5){
   if(mprojmean==0) jprojmean=1;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                  /*probs[i][jk][j1]= pp[jk]/pos;*/
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                }
   for(cptcov=1;cptcov<=i2;cptcov++){              else
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       k=k+1;            }
       fprintf(ficresf,"\n#******");          }
       for(j=1;j<=cptcoveff;j++) {          
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(jk=-1; jk <=nlstate+ndeath; jk++)
       }            for(m=-1; m <=nlstate+ndeath; m++)
       fprintf(ficresf,"******\n");              if(freq[jk][m][i] !=0 ) {
       fprintf(ficresf,"# StartingAge FinalAge");              if(first==1)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                      fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                    }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          if(i <= iagemax)
         fprintf(ficresf,"\n");            fprintf(ficresp,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            if(first==1)
             printf("Others in log...\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          fprintf(ficlog,"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        }
           nhstepm = nhstepm/hstepm;        /*}*/
              }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    dateintmean=dateintsum/k2cpt; 
           oldm=oldms;savm=savms;   
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fclose(ficresp);
            free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
           for (h=0; h<=nhstepm; h++){    free_vector(pp,1,nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    /* End of Freq */
             }  }
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;  /************ Prevalence ********************/
               for(i=1; i<=nlstate;i++) {                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)
                 if (mobilav==1)  {  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                 else {       in each health status at the date of interview (if between dateprev1 and dateprev2).
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       We still use firstpass and lastpass as another selection.
                 }    */
                   
               }    int i, m, jk, j1, bool, z1,j;
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);    double **prop;
                            double posprop; 
               }    double  y2; /* in fractional years */
             }    int iagemin, iagemax;
           }    int first; /** to stop verbosity which is redirected to log file */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    iagemin= (int) agemin;
       }    iagemax= (int) agemax;
     }    /*pp=vector(1,nlstate);*/
   }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
            /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    j1=0;
     
   fclose(ficresf);    /*j=cptcoveff;*/
 }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 /************** Forecasting ******************/    
 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){    first=1;
      for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      /*for(i1=1; i1<=ncodemax[k1];i1++){
   int *popage;        j1++;*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        
   double *popeffectif,*popcount;        for (i=1; i<=nlstate; i++)  
   double ***p3mat,***tabpop,***tabpopprev;          for(m=iagemin; m <= iagemax+3; m++)
   char filerespop[FILENAMELENGTH];            prop[i][m]=0.0;
        
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (i=1; i<=imx; i++) { /* Each individual */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          bool=1;
   agelim=AGESUP;          if  (cptcovn>0) {
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                bool=0;
            } 
            if (bool==1) { 
   strcpy(filerespop,"pop");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   strcat(filerespop,fileres);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     printf("Problem with forecast resultfile: %s\n", filerespop);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   printf("Computing forecasting: result on file '%s' \n", filerespop);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
   if (mobilav==1) {              }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            } /* end selection of waves */
     movingaverage(agedeb, fage, ageminpar, mobaverage);          }
   }        }
         for(i=iagemin; i <= iagemax+3; i++){  
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   if (stepm<=12) stepsize=1;            posprop += prop[jk][i]; 
            } 
   agelim=AGESUP;          
            for(jk=1; jk <=nlstate ; jk++){     
   hstepm=1;            if( i <=  iagemax){ 
   hstepm=hstepm/stepm;              if(posprop>=1.e-5){ 
                  probs[i][jk][j1]= prop[jk][i]/posprop;
   if (popforecast==1) {              } else{
     if((ficpop=fopen(popfile,"r"))==NULL) {                if(first==1){
       printf("Problem with population file : %s\n",popfile);exit(0);                  first=0;
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
     }                }
     popage=ivector(0,AGESUP);              }
     popeffectif=vector(0,AGESUP);            } 
     popcount=vector(0,AGESUP);          }/* end jk */ 
            }/* end i */ 
     i=1;        /*} *//* end i1 */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    } /* end j1 */
        
     imx=i;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    /*free_vector(pp,1,nlstate);*/
   }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  /************* Waves Concatenation ***************/
       k=k+1;  
       fprintf(ficrespop,"\n#******");  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)
       for(j=1;j<=cptcoveff;j++) {  {
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       }       Death is a valid wave (if date is known).
       fprintf(ficrespop,"******\n");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       fprintf(ficrespop,"# Age");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);       and mw[mi+1][i]. dh depends on stepm.
       if (popforecast==1)  fprintf(ficrespop," [Population]");       */
        
       for (cpt=0; cpt<=0;cpt++) {    int i, mi, m;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
               double sum=0., jmean=0.;*/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int first;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    int j, k=0,jk, ju, jl;
           nhstepm = nhstepm/hstepm;    double sum=0.;
              first=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    jmin=100000;
           oldm=oldms;savm=savms;    jmax=-1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      jmean=0.;
            for(i=1; i<=imx; i++){
           for (h=0; h<=nhstepm; h++){      mi=0;
             if (h==(int) (calagedate+YEARM*cpt)) {      m=firstpass;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      while(s[m][i] <= nlstate){
             }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
             for(j=1; j<=nlstate+ndeath;j++) {          mw[++mi][i]=m;
               kk1=0.;kk2=0;        if(m >=lastpass)
               for(i=1; i<=nlstate;i++) {                        break;
                 if (mobilav==1)        else
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          m++;
                 else {      }/* end while */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      if (s[m][i] > nlstate){
                 }        mi++;     /* Death is another wave */
               }        /* if(mi==0)  never been interviewed correctly before death */
               if (h==(int)(calagedate+12*cpt)){           /* Only death is a correct wave */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;        mw[mi][i]=m;
                   /*fprintf(ficrespop," %.3f", kk1);      }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }      wav[i]=mi;
             }      if(mi==0){
             for(i=1; i<=nlstate;i++){        nbwarn++;
               kk1=0.;        if(first==0){
                 for(j=1; j<=nlstate;j++){          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          first=1;
                 }        }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        if(first==1){
             }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      } /* end mi==0 */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    } /* End individuals */
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1; i<=imx; i++){
         }      for(mi=1; mi<wav[i];mi++){
       }        if (stepm <=0)
            dh[mi][i]=1;
   /******/        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            if (agedc[i] < 2*AGESUP) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              if(j==0) j=1;  /* Survives at least one month after exam */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              else if(j<0){
           nhstepm = nhstepm/hstepm;                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]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                j=1; /* Temporary Dangerous patch */
           oldm=oldms;savm=savms;                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);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  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]);
           for (h=0; h<=nhstepm; h++){                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);
             if (h==(int) (calagedate+YEARM*cpt)) {              }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              k=k+1;
             }              if (j >= jmax){
             for(j=1; j<=nlstate+ndeath;j++) {                jmax=j;
               kk1=0.;kk2=0;                ijmax=i;
               for(i=1; i<=nlstate;i++) {                            }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  if (j <= jmin){
               }                jmin=j;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                ijmin=i;
             }              }
           }              sum=sum+j;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       }            }
    }          }
   }          else{
              j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*        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]); */
   
   if (popforecast==1) {            k=k+1;
     free_ivector(popage,0,AGESUP);            if (j >= jmax) {
     free_vector(popeffectif,0,AGESUP);              jmax=j;
     free_vector(popcount,0,AGESUP);              ijmax=i;
   }            }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            else if (j <= jmin){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              jmin=j;
   fclose(ficrespop);              ijmin=i;
 }            }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 /***********************************************/            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
 /**************** Main Program *****************/            if(j<0){
 /***********************************************/              nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 int main(int argc, char *argv[])              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 {            }
             sum=sum+j;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          }
   double agedeb, agefin,hf;          jk= j/stepm;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
   double fret;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   double **xi,tmp,delta;            if(jl==0){
               dh[mi][i]=jk;
   double dum; /* Dummy variable */              bh[mi][i]=0;
   double ***p3mat;            }else{ /* We want a negative bias in order to only have interpolation ie
   int *indx;                    * to avoid the price of an extra matrix product in likelihood */
   char line[MAXLINE], linepar[MAXLINE];              dh[mi][i]=jk+1;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];              bh[mi][i]=ju;
   int firstobs=1, lastobs=10;            }
   int sdeb, sfin; /* Status at beginning and end */          }else{
   int c,  h , cpt,l;            if(jl <= -ju){
   int ju,jl, mi;              dh[mi][i]=jk;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              bh[mi][i]=jl;       /* bias is positive if real duration
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                                   * is higher than the multiple of stepm and negative otherwise.
   int mobilav=0,popforecast=0;                                   */
   int hstepm, nhstepm;            }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;            else{
               dh[mi][i]=jk+1;
   double bage, fage, age, agelim, agebase;              bh[mi][i]=ju;
   double ftolpl=FTOL;            }
   double **prlim;            if(dh[mi][i]==0){
   double *severity;              dh[mi][i]=1; /* At least one step */
   double ***param; /* Matrix of parameters */              bh[mi][i]=ju; /* At least one step */
   double  *p;              /*  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);*/
   double **matcov; /* Matrix of covariance */            }
   double ***delti3; /* Scale */          } /* end if mle */
   double *delti; /* Scale */        }
   double ***eij, ***vareij;      } /* end wave */
   double **varpl; /* Variances of prevalence limits by age */    }
   double *epj, vepp;    jmean=sum/k;
   double kk1, kk2;    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);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    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);
     }
   
   char *alph[]={"a","a","b","c","d","e"}, str[4];  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
   char z[1]="c", occ;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
 #include <sys/time.h>    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
 #include <time.h>     * Boring subroutine which should only output nbcode[Tvar[j]][k]
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       * nbcode[Tvar[j]][1]= 
   /* long total_usecs;    */
   struct timeval start_time, end_time;  
      int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    int modmaxcovj=0; /* Modality max of covariates j */
   getcwd(pathcd, size);    int cptcode=0; /* Modality max of covariates j */
     int modmincovj=0; /* Modality min of covariates j */
   printf("\n%s",version);  
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    cptcoveff=0; 
     scanf("%s",pathtot);   
   }    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   else{    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
     strcpy(pathtot,argv[1]);  
   }    /* Loop on covariates without age and products */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
   /*cygwin_split_path(pathtot,path,optionfile);      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/                                 modality of this covariate Vj*/ 
   /* cutv(path,optionfile,pathtot,'\\');*/        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                       * If product of Vn*Vm, still boolean *:
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   chdir(path);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   replace(pathc,path);                                        modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
 /*-------- arguments in the command line --------*/          modmaxcovj=ij; 
         else if (ij < modmincovj) 
   /* Log file */          modmincovj=ij; 
   strcat(filelog, optionfilefiname);        if ((ij < -1) && (ij > NCOVMAX)){
   strcat(filelog,".log");    /* */          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   if((ficlog=fopen(filelog,"w"))==NULL)    {          exit(1);
     printf("Problem with logfile %s\n",filelog);        }else
     goto end;        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 */
   fprintf(ficlog,"Log filename:%s\n",filelog);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   fprintf(ficlog,"\n%s",version);        /* getting the maximum value of the modality of the covariate
   fprintf(ficlog,"\nEnter the parameter file name: ");           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);           female is 1, then modmaxcovj=1.*/
   fflush(ficlog);      }
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   /* */      cptcode=modmaxcovj;
   strcpy(fileres,"r");      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   strcat(fileres, optionfilefiname);     /*for (i=0; i<=cptcode; i++) {*/
   strcat(fileres,".txt");    /* Other files have txt extension */      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
         printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   /*---------arguments file --------*/        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        }
     printf("Problem with optionfile %s\n",optionfile);        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     goto end;      } /* Ndum[-1] number of undefined modalities */
   }  
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   strcpy(filereso,"o");      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   strcat(filereso,fileres);      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
   if((ficparo=fopen(filereso,"w"))==NULL) {         modmincovj=3; modmaxcovj = 7;
     printf("Problem with Output resultfile: %s\n", filereso);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
     goto end;         variables V1_1 and V1_2.
   }         nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
   /* Reads comments: lines beginning with '#' */         nbcode[Tvar[j]][2]=1;
   while((c=getc(ficpar))=='#' && c!= EOF){         nbcode[Tvar[j]][3]=2;
     ungetc(c,ficpar);      */
     fgets(line, MAXLINE, ficpar);      ij=1; /* ij is similar to i but can jumps over null modalities */
     puts(line);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
     fputs(line,ficparo);        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   }          /*recode from 0 */
   ungetc(c,ficpar);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   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);                                       k is a modality. If we have model=V1+V1*sex 
   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);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   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);            ij++;
 while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);          if (ij > ncodemax[j]) break; 
     fgets(line, MAXLINE, ficpar);        }  /* end of loop on */
     puts(line);      } /* end of loop on modality */ 
     fputs(line,ficparo);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   }    
   ungetc(c,ficpar);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
      
        for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
   covar=matrix(0,NCOVMAX,1,n);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   cptcovn=0;     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;     Ndum[ij]++; 
    } 
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */   ij=1;
     for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   /* Read guess parameters */     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   /* Reads comments: lines beginning with '#' */     if((Ndum[i]!=0) && (i<=ncovcol)){
   while((c=getc(ficpar))=='#' && c!= EOF){       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
     ungetc(c,ficpar);       Tvaraff[ij]=i; /*For printing (unclear) */
     fgets(line, MAXLINE, ficpar);       ij++;
     puts(line);     }else
     fputs(line,ficparo);         Tvaraff[ij]=0;
   }   }
   ungetc(c,ficpar);   ij--;
     cptcoveff=ij; /*Number of total covariates*/
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)  }
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);  /*********** Health Expectancies ****************/
       if(mle==1)  
         printf("%1d%1d",i,j);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
       fprintf(ficlog,"%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){  {
         fscanf(ficpar," %lf",&param[i][j][k]);    /* Health expectancies, no variances */
         if(mle==1){    int i, j, nhstepm, hstepm, h, nstepm;
           printf(" %lf",param[i][j][k]);    int nhstepma, nstepma; /* Decreasing with age */
           fprintf(ficlog," %lf",param[i][j][k]);    double age, agelim, hf;
         }    double ***p3mat;
         else    double eip;
           fprintf(ficlog," %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);    pstamp(ficreseij);
       }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       fscanf(ficpar,"\n");    fprintf(ficreseij,"# Age");
       if(mle==1)    for(i=1; i<=nlstate;i++){
         printf("\n");      for(j=1; j<=nlstate;j++){
       fprintf(ficlog,"\n");        fprintf(ficreseij," e%1d%1d ",i,j);
       fprintf(ficparo,"\n");      }
     }      fprintf(ficreseij," e%1d. ",i);
      }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    fprintf(ficreseij,"\n");
   
   p=param[1][1];    
      if(estepm < stepm){
   /* Reads comments: lines beginning with '#' */      printf ("Problem %d lower than %d\n",estepm, stepm);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    else  hstepm=estepm;   
     fgets(line, MAXLINE, ficpar);    /* We compute the life expectancy from trapezoids spaced every estepm months
     puts(line);     * This is mainly to measure the difference between two models: for example
     fputs(line,ficparo);     * if stepm=24 months pijx are given only every 2 years and by summing them
   }     * we are calculating an estimate of the Life Expectancy assuming a linear 
   ungetc(c,ficpar);     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */     * to compare the new estimate of Life expectancy with the same linear 
   for(i=1; i <=nlstate; i++){     * hypothesis. A more precise result, taking into account a more precise
     for(j=1; j <=nlstate+ndeath-1; j++){     * curvature will be obtained if estepm is as small as stepm. */
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficparo,"%1d%1d",i1,j1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(k=1; k<=ncovmodel;k++){       nhstepm is the number of hstepm from age to agelim 
         fscanf(ficpar,"%le",&delti3[i][j][k]);       nstepm is the number of stepm from age to agelin. 
         printf(" %le",delti3[i][j][k]);       Look at hpijx to understand the reason of that which relies in memory size
         fprintf(ficparo," %le",delti3[i][j][k]);       and note for a fixed period like estepm months */
       }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fscanf(ficpar,"\n");       survival function given by stepm (the optimization length). Unfortunately it
       printf("\n");       means that if the survival funtion is printed only each two years of age and if
       fprintf(ficparo,"\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     }       results. So we changed our mind and took the option of the best precision.
   }    */
   delti=delti3[1][1];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
   /* Reads comments: lines beginning with '#' */    agelim=AGESUP;
   while((c=getc(ficpar))=='#' && c!= EOF){    /* If stepm=6 months */
     ungetc(c,ficpar);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     fgets(line, MAXLINE, ficpar);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     puts(line);      
     fputs(line,ficparo);  /* nhstepm age range expressed in number of stepm */
   }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   ungetc(c,ficpar);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      /* if (stepm >= YEARM) hstepm=1;*/
   matcov=matrix(1,npar,1,npar);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   for(i=1; i <=npar; i++){    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fscanf(ficpar,"%s",&str);  
     if(mle==1)    for (age=bage; age<=fage; age ++){ 
       printf("%s",str);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fprintf(ficlog,"%s",str);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fprintf(ficparo,"%s",str);      /* if (stepm >= YEARM) hstepm=1;*/
     for(j=1; j <=i; j++){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       fscanf(ficpar," %le",&matcov[i][j]);  
       if(mle==1){      /* If stepm=6 months */
         printf(" %.5le",matcov[i][j]);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         fprintf(ficlog," %.5le",matcov[i][j]);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       }      
       else      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         fprintf(ficlog," %.5le",matcov[i][j]);      
       fprintf(ficparo," %.5le",matcov[i][j]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     }      
     fscanf(ficpar,"\n");      printf("%d|",(int)age);fflush(stdout);
     if(mle==1)      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       printf("\n");      
     fprintf(ficlog,"\n");      /* Computing expectancies */
     fprintf(ficparo,"\n");      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++)
   for(i=1; i <=npar; i++)          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     for(j=i+1;j<=npar;j++)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       matcov[i][j]=matcov[j][i];            
                /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   if(mle==1)  
     printf("\n");          }
   fprintf(ficlog,"\n");  
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
     /*-------- Rewriting paramater file ----------*/        eip=0;
      strcpy(rfileres,"r");    /* "Rparameterfile */        for(j=1; j<=nlstate;j++){
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          eip +=eij[i][j][(int)age];
      strcat(rfileres,".");    /* */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        }
     if((ficres =fopen(rfileres,"w"))==NULL) {        fprintf(ficreseij,"%9.4f", eip );
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      }
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;      fprintf(ficreseij,"\n");
     }      
     fprintf(ficres,"#%s\n",version);    }
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /*-------- data file ----------*/    printf("\n");
     if((fic=fopen(datafile,"r"))==NULL)    {    fprintf(ficlog,"\n");
       printf("Problem with datafile: %s\n", datafile);goto end;    
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;  }
     }  
   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[] )
     n= lastobs;  
     severity = vector(1,maxwav);  {
     outcome=imatrix(1,maxwav+1,1,n);    /* Covariances of health expectancies eij and of total life expectancies according
     num=ivector(1,n);     to initial status i, ei. .
     moisnais=vector(1,n);    */
     annais=vector(1,n);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     moisdc=vector(1,n);    int nhstepma, nstepma; /* Decreasing with age */
     andc=vector(1,n);    double age, agelim, hf;
     agedc=vector(1,n);    double ***p3matp, ***p3matm, ***varhe;
     cod=ivector(1,n);    double **dnewm,**doldm;
     weight=vector(1,n);    double *xp, *xm;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double **gp, **gm;
     mint=matrix(1,maxwav,1,n);    double ***gradg, ***trgradg;
     anint=matrix(1,maxwav,1,n);    int theta;
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);        double eip, vip;
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     i=1;    xm=vector(1,npar);
     while (fgets(line, MAXLINE, fic) != NULL)    {    dnewm=matrix(1,nlstate*nlstate,1,npar);
       if ((i >= firstobs) && (i <=lastobs)) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
            
         for (j=maxwav;j>=1;j--){    pstamp(ficresstdeij);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
           strcpy(line,stra);    fprintf(ficresstdeij,"# Age");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1; i<=nlstate;i++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for(j=1; j<=nlstate;j++)
         }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
              fprintf(ficresstdeij," e%1d. ",i);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresstdeij,"\n");
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    pstamp(ficrescveij);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1; i<=nlstate;i++)
         for (j=ncovcol;j>=1;j--){      for(j=1; j<=nlstate;j++){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        cptj= (j-1)*nlstate+i;
         }        for(i2=1; i2<=nlstate;i2++)
         num[i]=atol(stra);          for(j2=1; j2<=nlstate;j2++){
                    cptj2= (j2-1)*nlstate+i2;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            if(cptj2 <= cptj)
           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;}*/              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
         i=i+1;      }
       }    fprintf(ficrescveij,"\n");
     }    
     /* printf("ii=%d", ij);    if(estepm < stepm){
        scanf("%d",i);*/      printf ("Problem %d lower than %d\n",estepm, stepm);
   imx=i-1; /* Number of individuals */    }
     else  hstepm=estepm;   
   /* for (i=1; i<=imx; i++){    /* We compute the life expectancy from trapezoids spaced every estepm months
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;     * This is mainly to measure the difference between two models: for example
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;     * if stepm=24 months pijx are given only every 2 years and by summing them
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;     * we are calculating an estimate of the Life Expectancy assuming a linear 
     }*/     * progression in between and thus overestimating or underestimating according
    /*  for (i=1; i<=imx; i++){     * to the curvature of the survival function. If, for the same date, we 
      if (s[4][i]==9)  s[4][i]=-1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      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]));}*/     * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
       * curvature will be obtained if estepm is as small as stepm. */
   /* 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 */    /* For example we decided to compute the life expectancy with the smallest unit */
   Tprod=ivector(1,15);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   Tvaraff=ivector(1,15);       nhstepm is the number of hstepm from age to agelim 
   Tvard=imatrix(1,15,1,2);       nstepm is the number of stepm from age to agelin. 
   Tage=ivector(1,15);             Look at hpijx to understand the reason of that which relies in memory size
           and note for a fixed period like estepm months */
   if (strlen(model) >1){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     j=0, j1=0, k1=1, k2=1;       survival function given by stepm (the optimization length). Unfortunately it
     j=nbocc(model,'+');       means that if the survival funtion is printed only each two years of age and if
     j1=nbocc(model,'*');       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     cptcovn=j+1;       results. So we changed our mind and took the option of the best precision.
     cptcovprod=j1;    */
        hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    /* If stepm=6 months */
       printf("Error. Non available option model=%s ",model);    /* nhstepm age range expressed in number of stepm */
       fprintf(ficlog,"Error. Non available option model=%s ",model);    agelim=AGESUP;
       goto end;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
     for(i=(j+1); i>=1;i--){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       /*scanf("%d",i);*/    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       if (strchr(strb,'*')) {  /* Model includes a product */    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/    gp=matrix(0,nhstepm,1,nlstate*nlstate);
         if (strcmp(strc,"age")==0) { /* Vn*age */    gm=matrix(0,nhstepm,1,nlstate*nlstate);
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    for (age=bage; age<=fage; age ++){ 
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           cptcovage++;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             Tage[cptcovage]=i;      /* if (stepm >= YEARM) hstepm=1;*/
             /*printf("stre=%s ", stre);*/      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         }  
         else if (strcmp(strd,"age")==0) { /* or age*Vn */      /* If stepm=6 months */
           cptcovprod--;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           cutv(strb,stre,strc,'V');         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           Tvar[i]=atoi(stre);      
           cptcovage++;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           Tage[cptcovage]=i;  
         }      /* Computing  Variances of health expectancies */
         else {  /* Age is not in the model */      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/         decrease memory allocation */
           Tvar[i]=ncovcol+k1;      for(theta=1; theta <=npar; theta++){
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */        for(i=1; i<=npar; i++){ 
           Tprod[k1]=i;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           Tvard[k1][1]=atoi(strc); /* m*/          xm[i] = x[i] - (i==theta ?delti[theta]:0);
           Tvard[k1][2]=atoi(stre); /* n */        }
           Tvar[cptcovn+k2]=Tvard[k1][1];        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
           for (k=1; k<=lastobs;k++)    
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        for(j=1; j<= nlstate; j++){
           k1++;          for(i=1; i<=nlstate; i++){
           k2=k2+2;            for(h=0; h<=nhstepm-1; h++){
         }              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
       }              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       else { /* no more sum */            }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          }
        /*  scanf("%d",i);*/        }
       cutv(strd,strc,strb,'V');       
       Tvar[i]=atoi(strc);        for(ij=1; ij<= nlstate*nlstate; ij++)
       }          for(h=0; h<=nhstepm-1; h++){
       strcpy(modelsav,stra);              gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          }
         scanf("%d",i);*/      }/* End theta */
     } /* end of loop + */      
   } /* end model */      
        for(h=0; h<=nhstepm-1; h++)
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        for(j=1; j<=nlstate*nlstate;j++)
   printf("cptcovprod=%d ", cptcovprod);          for(theta=1; theta <=npar; theta++)
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);            trgradg[h][j][theta]=gradg[h][theta][j];
   scanf("%d ",i);*/      
     fclose(fic);  
        for(ij=1;ij<=nlstate*nlstate;ij++)
     /*  if(mle==1){*/        for(ji=1;ji<=nlstate*nlstate;ji++)
     if (weightopt != 1) { /* Maximisation without weights*/          varhe[ij][ji][(int)age] =0.;
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }       printf("%d|",(int)age);fflush(stdout);
     /*-calculation of age at interview from date of interview and age at death -*/       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     agev=matrix(1,maxwav,1,imx);       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
     for (i=1; i<=imx; i++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       for(m=2; (m<= maxwav); m++) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          for(ij=1;ij<=nlstate*nlstate;ij++)
          anint[m][i]=9999;            for(ji=1;ji<=nlstate*nlstate;ji++)
          s[m][i]=-1;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }        }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;      }
       }  
     }      /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for (i=1; i<=imx; i++)  {      for(i=1; i<=nlstate;i++)
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for(j=1; j<=nlstate;j++)
       for(m=1; (m<= maxwav); m++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         if(s[m][i] >0){            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
           if (s[m][i] >= nlstate+1) {            
             if(agedc[i]>0)            /* 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]);*/
               if(moisdc[i]!=99 && andc[i]!=9999)  
                 agev[m][i]=agedc[i];          }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {      fprintf(ficresstdeij,"%3.0f",age );
               if (andc[i]!=9999){      for(i=1; i<=nlstate;i++){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        eip=0.;
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);        vip=0.;
               agev[m][i]=-1;        for(j=1; j<=nlstate;j++){
               }          eip += eij[i][j][(int)age];
             }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
           }            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           else if(s[m][i] !=9){ /* Should no more exist */          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        }
             if(mint[m][i]==99 || anint[m][i]==9999)        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
               agev[m][i]=1;      }
             else if(agev[m][i] <agemin){      fprintf(ficresstdeij,"\n");
               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);*/      fprintf(ficrescveij,"%3.0f",age );
             }      for(i=1; i<=nlstate;i++)
             else if(agev[m][i] >agemax){        for(j=1; j<=nlstate;j++){
               agemax=agev[m][i];          cptj= (j-1)*nlstate+i;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          for(i2=1; i2<=nlstate;i2++)
             }            for(j2=1; j2<=nlstate;j2++){
             /*agev[m][i]=anint[m][i]-annais[i];*/              cptj2= (j2-1)*nlstate+i2;
             /*   agev[m][i] = age[i]+2*m;*/              if(cptj2 <= cptj)
           }                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
           else { /* =9 */            }
             agev[m][i]=1;        }
             s[m][i]=-1;      fprintf(ficrescveij,"\n");
           }     
         }    }
         else /*= 0 Unknown */    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           agev[m][i]=1;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     }    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for (i=1; i<=imx; i++)  {    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(m=1; (m<= maxwav); m++){    printf("\n");
         if (s[m][i] > (nlstate+ndeath)) {    fprintf(ficlog,"\n");
           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);      free_vector(xm,1,npar);
           goto end;    free_vector(xp,1,npar);
         }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
 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);  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
     free_vector(severity,1,maxwav);  {
     free_imatrix(outcome,1,maxwav+1,1,n);    /* Variance of health expectancies */
     free_vector(moisnais,1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     free_vector(annais,1,n);    /* double **newm;*/
     /* free_matrix(mint,1,maxwav,1,n);    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
        free_matrix(anint,1,maxwav,1,n);*/    
     free_vector(moisdc,1,n);    int movingaverage();
     free_vector(andc,1,n);    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
        int i, j, nhstepm, hstepm, h, nstepm ;
     wav=ivector(1,imx);    int k;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double *xp;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    double **gp, **gm;  /* for var eij */
        double ***gradg, ***trgradg; /*for var eij */
     /* Concatenates waves */    double **gradgp, **trgradgp; /* for var p point j */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
       Tcode=ivector(1,100);    double age,agelim, hf;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    double ***mobaverage;
       ncodemax[1]=1;    int theta;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    char digit[4];
          char digitp[25];
    codtab=imatrix(1,100,1,10);  
    h=0;    char fileresprobmorprev[FILENAMELENGTH];
    m=pow(2,cptcoveff);  
      if(popbased==1){
    for(k=1;k<=cptcoveff; k++){      if(mobilav!=0)
      for(i=1; i <=(m/pow(2,k));i++){        strcpy(digitp,"-populbased-mobilav-");
        for(j=1; j <= ncodemax[k]; j++){      else strcpy(digitp,"-populbased-nomobil-");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    }
            h++;    else 
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      strcpy(digitp,"-stablbased-");
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  
          }    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("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       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);    strcpy(fileresprobmorprev,"prmorprev"); 
       }    sprintf(digit,"%-d",ij);
       printf("\n");    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       scanf("%d",i);*/    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
        strcat(fileresprobmorprev,fileres);
    /* Calculates basic frequencies. Computes observed prevalence at single age    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        and prints on file fileres'p'. */      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
        }
        printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficresprobmorprev);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    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);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
          for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     /* For Powell, parameters are in a vector p[] starting at p[1]      fprintf(ficresprobmorprev," p.%-d SE",j);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      for(i=1; i<=nlstate;i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     if(mle==1){    fprintf(ficresprobmorprev,"\n");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    fprintf(ficgp,"\n# Routine varevsij");
     }    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
        fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     /*--------- results files --------------*/    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     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);  /*   } */
      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
    jk=1;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    if(popbased==1)
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      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(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    else
    for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
      for(k=1; k <=(nlstate+ndeath); k++){    fprintf(ficresvij,"# Age");
        if (k != i)    for(i=1; i<=nlstate;i++)
          {      for(j=1; j<=nlstate;j++)
            printf("%d%d ",i,k);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
            fprintf(ficlog,"%d%d ",i,k);    fprintf(ficresvij,"\n");
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    xp=vector(1,npar);
              printf("%f ",p[jk]);    dnewm=matrix(1,nlstate,1,npar);
              fprintf(ficlog,"%f ",p[jk]);    doldm=matrix(1,nlstate,1,nlstate);
              fprintf(ficres,"%f ",p[jk]);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
              jk++;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            }  
            printf("\n");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
            fprintf(ficlog,"\n");    gpp=vector(nlstate+1,nlstate+ndeath);
            fprintf(ficres,"\n");    gmp=vector(nlstate+1,nlstate+ndeath);
          }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      }    
    }    if(estepm < stepm){
    if(mle==1){      printf ("Problem %d lower than %d\n",estepm, stepm);
      /* Computing hessian and covariance matrix */    }
      ftolhess=ftol; /* Usually correct */    else  hstepm=estepm;   
      hesscov(matcov, p, npar, delti, ftolhess, func);    /* 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. 
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");       nhstepm is the number of hstepm from age to agelim 
    printf("# Scales (for hessian or gradient estimation)\n");       nstepm is the number of stepm from age to agelin. 
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");       Look at function hpijx to understand why (it is linked to memory size questions) */
    for(i=1,jk=1; i <=nlstate; i++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      for(j=1; j <=nlstate+ndeath; j++){       survival function given by stepm (the optimization length). Unfortunately it
        if (j!=i) {       means that if the survival funtion is printed every two years of age and if
          fprintf(ficres,"%1d%1d",i,j);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
          printf("%1d%1d",i,j);       results. So we changed our mind and took the option of the best precision.
          fprintf(ficlog,"%1d%1d",i,j);    */
          for(k=1; k<=ncovmodel;k++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
            printf(" %.5e",delti[jk]);    agelim = AGESUP;
            fprintf(ficlog," %.5e",delti[jk]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
            fprintf(ficres," %.5e",delti[jk]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
            jk++;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          printf("\n");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          fprintf(ficlog,"\n");      gp=matrix(0,nhstepm,1,nlstate);
          fprintf(ficres,"\n");      gm=matrix(0,nhstepm,1,nlstate);
        }  
      }  
    }      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
    k=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    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)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      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");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    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");  
    for(i=1;i<=npar;i++){        if (popbased==1) {
      /*  if (k>nlstate) k=1;          if(mobilav ==0){
          i1=(i-1)/(ncovmodel*nlstate)+1;            for(i=1; i<=nlstate;i++)
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              prlim[i][i]=probs[(int)age][i][ij];
          printf("%s%d%d",alph[k],i1,tab[i]);*/          }else{ /* mobilav */ 
      fprintf(ficres,"%3d",i);            for(i=1; i<=nlstate;i++)
      if(mle==1)              prlim[i][i]=mobaverage[(int)age][i][ij];
        printf("%3d",i);          }
      fprintf(ficlog,"%3d",i);        }
      for(j=1; j<=i;j++){    
        fprintf(ficres," %.5e",matcov[i][j]);        for(j=1; j<= nlstate; j++){
        if(mle==1)          for(h=0; h<=nhstepm; h++){
          printf(" %.5e",matcov[i][j]);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
        fprintf(ficlog," %.5e",matcov[i][j]);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
      }          }
      fprintf(ficres,"\n");        }
      if(mle==1)        /* This for computing probability of death (h=1 means
        printf("\n");           computed over hstepm matrices product = hstepm*stepm months) 
      fprintf(ficlog,"\n");           as a weighted average of prlim.
      k++;        */
    }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              for(i=1,gpp[j]=0.; i<= nlstate; i++)
    while((c=getc(ficpar))=='#' && c!= EOF){            gpp[j] += prlim[i][i]*p3mat[i][j][1];
      ungetc(c,ficpar);        }    
      fgets(line, MAXLINE, ficpar);        /* end probability of death */
      puts(line);  
      fputs(line,ficparo);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
    }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
    ungetc(c,ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    estepm=0;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    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 (popbased==1) {
    if (fage <= 2) {          if(mobilav ==0){
      bage = ageminpar;            for(i=1; i<=nlstate;i++)
      fage = agemaxpar;              prlim[i][i]=probs[(int)age][i][ij];
    }          }else{ /* mobilav */ 
                for(i=1; i<=nlstate;i++)
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          }
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        }
      
    while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
      ungetc(c,ficpar);          for(h=0; h<=nhstepm; h++){
      fgets(line, MAXLINE, ficpar);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
      puts(line);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
      fputs(line,ficparo);          }
    }        }
    ungetc(c,ficpar);        /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);           as a weighted average of prlim.
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        */
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              for(i=1,gmp[j]=0.; i<= nlstate; i++)
    while((c=getc(ficpar))=='#' && c!= EOF){           gmp[j] += prlim[i][i]*p3mat[i][j][1];
      ungetc(c,ficpar);        }    
      fgets(line, MAXLINE, ficpar);        /* end probability of death */
      puts(line);  
      fputs(line,ficparo);        for(j=1; j<= nlstate; j++) /* vareij */
    }          for(h=0; h<=nhstepm; h++){
    ungetc(c,ficpar);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
   fprintf(ficparo,"pop_based=%d\n",popbased);        } /* End theta */
   fprintf(ficres,"pop_based=%d\n",popbased);    
        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for(h=0; h<=nhstepm; h++) /* veij */
     fgets(line, MAXLINE, ficpar);        for(j=1; j<=nlstate;j++)
     puts(line);          for(theta=1; theta <=npar; theta++)
     fputs(line,ficparo);            trgradg[h][j][theta]=gradg[h][theta][j];
   }  
   ungetc(c,ficpar);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
   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);          trgradgp[j][theta]=gradgp[theta][j];
 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(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
 while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1;j<=nlstate;j++)
     ungetc(c,ficpar);          vareij[i][j][(int)age] =0.;
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(h=0;h<=nhstepm;h++){
     fputs(line,ficparo);        for(k=0;k<=nhstepm;k++){
   }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   ungetc(c,ficpar);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            for(j=1;j<=nlstate;j++)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }
       }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
       /* pptj */
 /*------------ gnuplot -------------*/      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   strcpy(optionfilegnuplot,optionfilefiname);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   strcat(optionfilegnuplot,".gp");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     printf("Problem with file %s",optionfilegnuplot);          varppt[j][i]=doldmp[j][i];
   }      /* end ppptj */
   fclose(ficgp);      /*  x centered again */
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 /*--------- index.htm --------*/      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
   strcpy(optionfilehtm,optionfile);      if (popbased==1) {
   strcat(optionfilehtm,".htm");        if(mobilav ==0){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          for(i=1; i<=nlstate;i++)
     printf("Problem with %s \n",optionfilehtm), exit(0);            prlim[i][i]=probs[(int)age][i][ij];
   }        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            prlim[i][i]=mobaverage[(int)age][i][ij];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        }
 \n      }
 Total number of observations=%d <br>\n               
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      /* This for computing probability of death (h=1 means
 <hr  size=\"2\" color=\"#EC5E5E\">         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
  <ul><li><h4>Parameter files</h4>\n         as a weighted average of prlim.
  - 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      for(j=nlstate+1;j<=nlstate+ndeath;j++){
  - 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);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   fclose(fichtm);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);      /* end probability of death */
    
 /*------------ free_vector  -------------*/      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
  chdir(path);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
  free_ivector(wav,1,imx);        for(i=1; i<=nlstate;i++){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          }
  free_ivector(num,1,n);      } 
  free_vector(agedc,1,n);      fprintf(ficresprobmorprev,"\n");
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  
  fclose(ficparo);      fprintf(ficresvij,"%.0f ",age );
  fclose(ficres);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   /*--------------- Prevalence limit --------------*/        }
        fprintf(ficresvij,"\n");
   strcpy(filerespl,"pl");      free_matrix(gp,0,nhstepm,1,nlstate);
   strcat(filerespl,fileres);      free_matrix(gm,0,nhstepm,1,nlstate);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    } /* End age */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    free_vector(gpp,nlstate+1,nlstate+ndeath);
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    free_vector(gmp,nlstate+1,nlstate+ndeath);
   fprintf(ficrespl,"#Prevalence limit\n");    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   fprintf(ficrespl,"#Age ");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
   fprintf(ficrespl,"\n");    /* 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)\";");
   prlim=matrix(1,nlstate,1,nlstate);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
   k=0;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   agebase=ageminpar;    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);
   agelim=agemaxpar;    /*  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);
   ftolpl=1.e-10;  */
   i1=cptcoveff;  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   if (cptcovn < 1){i1=1;}    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
   for(cptcov=1;cptcov<=i1;cptcov++){    free_vector(xp,1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(doldm,1,nlstate,1,nlstate);
         k=k+1;    free_matrix(dnewm,1,nlstate,1,npar);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficrespl,"\n#******");    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         printf("\n#******");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficlog,"\n#******");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(j=1;j<=cptcoveff;j++) {    fclose(ficresprobmorprev);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fflush(ficgp);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fflush(fichtm); 
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  }  /* end varevsij */
         }  
         fprintf(ficrespl,"******\n");  /************ Variance of prevlim ******************/
         printf("******\n");  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,"******\n");  {
            /* Variance of prevalence limit */
         for (age=agebase; age<=agelim; age++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );    double **dnewm,**doldm;
           for(i=1; i<=nlstate;i++)    int i, j, nhstepm, hstepm;
           fprintf(ficrespl," %.5f", prlim[i][i]);    double *xp;
           fprintf(ficrespl,"\n");    double *gp, *gm;
         }    double **gradg, **trgradg;
       }    double age,agelim;
     }    int theta;
   fclose(ficrespl);    
     pstamp(ficresvpl);
   /*------------- h Pij x at various ages ------------*/    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
      fprintf(ficresvpl,"# Age");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    for(i=1; i<=nlstate;i++)
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        fprintf(ficresvpl," %1d-%1d",i,i);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    fprintf(ficresvpl,"\n");
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }    xp=vector(1,npar);
   printf("Computing pij: result on file '%s' \n", filerespij);    dnewm=matrix(1,nlstate,1,npar);
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);    doldm=matrix(1,nlstate,1,nlstate);
      
   stepsize=(int) (stepm+YEARM-1)/YEARM;    hstepm=1*YEARM; /* Every year of age */
   /*if (stepm<=24) stepsize=2;*/    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
   agelim=AGESUP;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   hstepm=stepsize*YEARM; /* Every year of age */      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   /* hstepm=1;   aff par mois*/      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
   k=0;      gm=vector(1,nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(theta=1; theta <=npar; theta++){
       k=k+1;        for(i=1; i<=npar; i++){ /* Computes gradient */
         fprintf(ficrespij,"\n#****** ");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         for(j=1;j<=cptcoveff;j++)        }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fprintf(ficrespij,"******\n");        for(i=1;i<=nlstate;i++)
                  gp[i] = prlim[i][i];
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(i=1; i<=npar; i++) /* Computes gradient */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;        for(i=1;i<=nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           fprintf(ficrespij,"# Age");      } /* End theta */
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)      trgradg =matrix(1,nlstate,1,npar);
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");      for(j=1; j<=nlstate;j++)
            for (h=0; h<=nhstepm; h++){        for(theta=1; theta <=npar; theta++)
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          trgradg[j][theta]=gradg[theta][j];
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)      for(i=1;i<=nlstate;i++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        varpl[i][(int)age] =0.;
             fprintf(ficrespij,"\n");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
              }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i=1;i<=nlstate;i++)
           fprintf(ficrespij,"\n");        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]));
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
   fclose(ficrespij);      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
   /*---------- Forecasting ------------------*/    } /* End age */
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    free_vector(xp,1,npar);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    free_matrix(doldm,1,nlstate,1,npar);
   }    free_matrix(dnewm,1,nlstate,1,nlstate);
   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);  /************ 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;
   /*---------- Health expectancies and variances ------------*/    int k2, l2, j1,  z1;
     int k=0, l;
   strcpy(filerest,"t");    int first=1, first1, first2;
   strcat(filerest,fileres);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   if((ficrest=fopen(filerest,"w"))==NULL) {    double **dnewm,**doldm;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    double *xp;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    double *gp, *gm;
   }    double **gradg, **trgradg;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double **mu;
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
   strcpy(filerese,"e");    char fileresprob[FILENAMELENGTH];
   strcat(filerese,fileres);    char fileresprobcov[FILENAMELENGTH];
   if((ficreseij=fopen(filerese,"w"))==NULL) {    char fileresprobcor[FILENAMELENGTH];
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double ***varpij;
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }    strcpy(fileresprob,"prob"); 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    strcat(fileresprob,fileres);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
   strcpy(fileresv,"v");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   strcat(fileresv,fileres);    }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    strcpy(fileresprobcov,"probcov"); 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    strcat(fileresprobcov,fileres);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcov);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    }
   calagedate=-1;    strcpy(fileresprobcor,"probcor"); 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   k=0;      printf("Problem with resultfile: %s\n", fileresprobcor);
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       fprintf(ficrest,"\n#****** ");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       for(j=1;j<=cptcoveff;j++)    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       fprintf(ficrest,"******\n");    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);
       fprintf(ficreseij,"\n#****** ");    pstamp(ficresprob);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprob,"# Age");
       fprintf(ficreseij,"******\n");    pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       fprintf(ficresvij,"\n#****** ");    fprintf(ficresprobcov,"# Age");
       for(j=1;j<=cptcoveff;j++)    pstamp(ficresprobcor);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       fprintf(ficresvij,"******\n");    fprintf(ficresprobcor,"# Age");
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    for(i=1; i<=nlstate;i++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        for(j=1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       oldm=oldms;savm=savms;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);      }  
       if(popbased==1){   /* fprintf(ficresprob,"\n");
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);    fprintf(ficresprobcov,"\n");
        }    fprintf(ficresprobcor,"\n");
    */
      xp=vector(1,npar);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       fprintf(ficrest,"\n");    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       epj=vector(1,nlstate+1);    first=1;
       for(age=bage; age <=fage ;age++){    fprintf(ficgp,"\n# Routine varprob");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         if (popbased==1) {    fprintf(fichtm,"\n");
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][k];    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(ficrest," %4.0f",age);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  and drawn. It helps understanding how is the covariance between two incidences.\
           for(i=1, epj[j]=0.;i <=nlstate;i++) {   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    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. \
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/  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 \
           epj[nlstate+1] +=epj[j];  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>\
         for(i=1, vepp=0.;i <=nlstate;i++)  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];    cov[1]=1;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    /* tj=cptcoveff; */
         for(j=1;j <=nlstate;j++){    tj = (int) pow(2,cptcoveff);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         }    j1=0;
         fprintf(ficrest,"\n");    for(j1=1; j1<=tj;j1++){
       }      /*for(i1=1; i1<=ncodemax[t];i1++){ */
     }      /*j1++;*/
   }        if  (cptcovn>0) {
 free_matrix(mint,1,maxwav,1,n);          fprintf(ficresprob, "\n#********** Variable "); 
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(weight,1,n);          fprintf(ficresprob, "**********\n#\n");
   fclose(ficreseij);          fprintf(ficresprobcov, "\n#********** Variable "); 
   fclose(ficresvij);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fclose(ficrest);          fprintf(ficresprobcov, "**********\n#\n");
   fclose(ficpar);          
   free_vector(epj,1,nlstate+1);          fprintf(ficgp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*------- Variance limit prevalence------*/            fprintf(ficgp, "**********\n#\n");
           
   strcpy(fileresvpl,"vpl");          
   strcat(fileresvpl,fileres);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     exit(0);          
   }          fprintf(ficresprobcor, "\n#********** Variable ");    
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){        
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       k=k+1;        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       fprintf(ficresvpl,"\n#****** ");        gp=vector(1,(nlstate)*(nlstate+ndeath));
       for(j=1;j<=cptcoveff;j++)        gm=vector(1,(nlstate)*(nlstate+ndeath));
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for (age=bage; age<=fage; age ++){ 
       fprintf(ficresvpl,"******\n");          cov[2]=age;
                for (k=1; k<=cptcovn;k++) {
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
       oldm=oldms;savm=savms;                                                           * 1  1 1 1 1
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                                                           * 2  2 1 1 1
     }                                                           * 3  1 2 1 1
  }                                                           */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
   fclose(ficresvpl);          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*---------- End : free ----------------*/          for (k=1; k<=cptcovprod;k++)
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++)
                xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);            
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            k=0;
              for(i=1; i<= (nlstate); i++){
   free_matrix(matcov,1,npar,1,npar);              for(j=1; j<=(nlstate+ndeath);j++){
   free_vector(delti,1,npar);                k=k+1;
   free_matrix(agev,1,maxwav,1,imx);                gp[k]=pmmij[i][j];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);              }
             }
   fprintf(fichtm,"\n</body>");            
   fclose(fichtm);            for(i=1; i<=npar; i++)
   fclose(ficgp);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
        
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   if(erreur >0){            k=0;
     printf("End of Imach with error or warning %d\n",erreur);            for(i=1; i<=(nlstate); i++){
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);              for(j=1; j<=(nlstate+ndeath);j++){
   }else{                k=k+1;
    printf("End of Imach\n");                gm[k]=pmmij[i][j];
    fprintf(ficlog,"End of Imach\n");              }
   }            }
   printf("See log file on %s\n",filelog);       
   fclose(ficlog);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
            }
   /* 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);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   /*------ End -----------*/            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
  end:          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
 #ifdef windows          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   /* chdir(pathcd);*/  
 #endif          pmij(pmmij,cov,ncovmodel,x,nlstate);
  /*system("wgnuplot graph.plt");*/          
  /*system("../gp37mgw/wgnuplot graph.plt");*/          k=0;
  /*system("cd ../gp37mgw");*/          for(i=1; i<=(nlstate); i++){
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            for(j=1; j<=(nlstate+ndeath);j++){
  strcpy(plotcmd,GNUPLOTPROGRAM);              k=k+1;
  strcat(plotcmd," ");              mu[k][(int) age]=pmmij[i][j];
  strcat(plotcmd,optionfilegnuplot);            }
  system(plotcmd);          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
 #ifdef windows            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   while (z[0] != 'q') {              varpij[i][j][(int)age] = doldm[i][j];
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          /*printf("\n%d ",(int)age);
     scanf("%s",z);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     if (z[0] == 'c') system("./imach");            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     else if (z[0] == 'e') system(optionfilehtm);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     else if (z[0] == 'g') system(plotcmd);            }*/
     else if (z[0] == 'q') exit(0);  
   }          fprintf(ficresprob,"\n%d ",(int)age);
 #endif          fprintf(ficresprobcov,"\n%d ",(int)age);
 }          fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
           /* command line Intel compiler 64bit windows:
           /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" */
           /*
           /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" */
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           return 0;
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
           return 0;
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
   #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*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
   #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.1.50  
changed lines
  Added in v.1.184


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