Diff for /imach/src/imach.c between versions 1.47 and 1.190

version 1.47, 2002/06/10 13:12:01 version 1.190, 2015/05/05 08:51:13
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.190  2015/05/05 08:51:13  brouard
      Summary: Adding digits in output parameters (7 digits instead of 6)
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Fix 1+age+.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.189  2015/04/30 14:45:16  brouard
   case of a health survey which is our main interest) -2- at least a    Summary: 0.98q2
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.188  2015/04/30 08:27:53  brouard
   computed from the time spent in each health state according to a    *** empty log message ***
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.187  2015/04/29 09:11:15  brouard
   simplest model is the multinomial logistic model where pij is the    *** empty log message ***
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.186  2015/04/23 12:01:52  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: V1*age is working now, version 0.98q1
   '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    Some codes had been disabled in order to simplify and Vn*age was
   where the markup *Covariates have to be included here again* invites    working in the optimization phase, ie, giving correct MLE parameters,
   you to do it.  More covariates you add, slower the    but, as usual, outputs were not correct and program core dumped.
   convergence.  
     Revision 1.185  2015/03/11 13:26:42  brouard
   The advantage of this computer programme, compared to a simple    Summary: Inclusion of compile and links command line for Intel Compiler
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.184  2015/03/11 11:52:39  brouard
   intermediate interview, the information is lost, but taken into    Summary: Back from Windows 8. Intel Compiler
   account using an interpolation or extrapolation.    
     Revision 1.183  2015/03/10 20:34:32  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: 0.98q0, trying with directest, mnbrak fixed
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    We use directest instead of original Powell test; probably no
   states. This elementary transition (by month or quarter trimester,    incidence on the results, but better justifications;
   semester or year) is model as a multinomial logistic.  The hPx    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   matrix is simply the matrix product of nh*stepm elementary matrices    wrong results.
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.182  2015/02/12 08:19:57  brouard
     Summary: Trying to keep directest which seems simpler and more general
   Also this programme outputs the covariance matrix of the parameters but also    Author: Nicolas Brouard
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.181  2015/02/11 23:22:24  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Summary: Comments on Powell added
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Author:
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.180  2015/02/11 17:33:45  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.179  2015/01/04 09:57:06  brouard
      Summary: back to OS/X
 #include <math.h>  
 #include <stdio.h>    Revision 1.178  2015/01/04 09:35:48  brouard
 #include <stdlib.h>    *** empty log message ***
 #include <unistd.h>  
     Revision 1.177  2015/01/03 18:40:56  brouard
 #define MAXLINE 256    Summary: Still testing ilc32 on OSX
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.176  2015/01/03 16:45:04  brouard
 #define FILENAMELENGTH 80    *** empty log message ***
 /*#define DEBUG*/  
 #define windows    Revision 1.175  2015/01/03 16:33:42  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    *** empty log message ***
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.174  2015/01/03 16:15:49  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: Still in cross-compilation
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.173  2015/01/03 12:06:26  brouard
 #define NINTERVMAX 8    Summary: trying to detect cross-compilation
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.172  2014/12/27 12:07:47  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.171  2014/12/23 13:26:59  brouard
 #define AGESUP 130    Summary: Back from Visual C
 #define AGEBASE 40  
 #ifdef windows    Still problem with utsname.h on Windows
 #define DIRSEPARATOR '\\'  
 #else    Revision 1.170  2014/12/23 11:17:12  brouard
 #define DIRSEPARATOR '/'    Summary: Cleaning some \%% back to %%
 #endif  
     The escape was mandatory for a specific compiler (which one?), but too many warnings.
 char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    Revision 1.169  2014/12/22 23:08:31  brouard
 int nvar;    Summary: 0.98p
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.168  2014/12/22 15:17:42  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Summary: update
 int popbased=0;  
     Revision 1.167  2014/12/22 13:50:56  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Summary: Testing uname and compiler version and if compiled 32 or 64
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Testing on Linux 64
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.166  2014/12/22 11:40:47  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    *** empty log message ***
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.165  2014/12/16 11:20:36  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Summary: After compiling on Visual C
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    * imach.c (Module): Merging 1.61 to 1.162
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;    Revision 1.164  2014/12/16 10:52:11  brouard
 char filerese[FILENAMELENGTH];    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 FILE  *ficresvij;  
 char fileresv[FILENAMELENGTH];    * imach.c (Module): Merging 1.61 to 1.162
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Revision 1.163  2014/12/16 10:30:11  brouard
 char title[MAXLINE];    * imach.c (Module): Merging 1.61 to 1.162
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Revision 1.162  2014/09/25 11:43:39  brouard
     Summary: temporary backup 0.99!
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
     Revision 1.1  2014/09/16 11:06:58  brouard
 char filerest[FILENAMELENGTH];    Summary: With some code (wrong) for nlopt
 char fileregp[FILENAMELENGTH];  
 char popfile[FILENAMELENGTH];    Author:
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.160  2014/09/02 09:24:05  brouard
 #define FTOL 1.0e-10    *** empty log message ***
   
 #define NRANSI    Revision 1.159  2014/09/01 10:34:10  brouard
 #define ITMAX 200    Summary: WIN32
     Author: Brouard
 #define TOL 2.0e-4  
     Revision 1.158  2014/08/27 17:11:51  brouard
 #define CGOLD 0.3819660    *** empty log message ***
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.157  2014/08/27 16:26:55  brouard
     Summary: Preparing windows Visual studio version
 #define GOLD 1.618034    Author: Brouard
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    In order to compile on Visual studio, time.h is now correct and time_t
     and tm struct should be used. difftime should be used but sometimes I
 static double maxarg1,maxarg2;    just make the differences in raw time format (time(&now).
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Trying to suppress #ifdef LINUX
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Add xdg-open for __linux in order to open default browser.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.156  2014/08/25 20:10:10  brouard
 #define rint(a) floor(a+0.5)    *** empty log message ***
   
 static double sqrarg;    Revision 1.155  2014/08/25 18:32:34  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Summary: New compile, minor changes
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Author: Brouard
   
 int imx;    Revision 1.154  2014/06/20 17:32:08  brouard
 int stepm;    Summary: Outputs now all graphs of convergence to period prevalence
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.153  2014/06/20 16:45:46  brouard
 int estepm;    Summary: If 3 live state, convergence to period prevalence on same graph
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Author: Brouard
   
 int m,nb;    Revision 1.152  2014/06/18 17:54:09  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.151  2014/06/18 16:43:30  brouard
 double dateintmean=0;    *** empty log message ***
   
 double *weight;    Revision 1.150  2014/06/18 16:42:35  brouard
 int **s; /* Status */    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 double *agedc, **covar, idx;    Author: brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.149  2014/06/18 15:51:14  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Summary: Some fixes in parameter files errors
 double ftolhess; /* Tolerance for computing hessian */    Author: Nicolas Brouard
   
 /**************** split *************************/    Revision 1.148  2014/06/17 17:38:48  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Summary: Nothing new
 {    Author: Brouard
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Just a new packaging for OS/X version 0.98nS
   
    l1 = strlen( path );                 /* length of path */    Revision 1.147  2014/06/16 10:33:11  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    *** empty log message ***
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.146  2014/06/16 10:20:28  brouard
 #if     defined(__bsd__)                /* get current working directory */    Summary: Merge
       extern char       *getwd( );    Author: Brouard
   
       if ( getwd( dirc ) == NULL ) {    Merge, before building revised version.
 #else  
       extern char       *getcwd( );    Revision 1.145  2014/06/10 21:23:15  brouard
     Summary: Debugging with valgrind
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Author: Nicolas Brouard
 #endif  
          return( GLOCK_ERROR_GETCWD );    Lot of changes in order to output the results with some covariates
       }    After the Edimburgh REVES conference 2014, it seems mandatory to
       strcpy( name, path );             /* we've got it */    improve the code.
    } else {                             /* strip direcotry from path */    No more memory valgrind error but a lot has to be done in order to
       s++;                              /* after this, the filename */    continue the work of splitting the code into subroutines.
       l2 = strlen( s );                 /* length of filename */    Also, decodemodel has been improved. Tricode is still not
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    optimal. nbcode should be improved. Documentation has been added in
       strcpy( name, s );                /* save file name */    the source code.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.143  2014/01/26 09:45:38  brouard
    }    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.142  2014/01/26 03:57:36  brouard
 #endif    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    s = strrchr( name, '.' );            /* find last / */  
    s++;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.141  2014/01/26 02:42:01  brouard
    l2= strlen( s)+1;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.140  2011/09/02 10:37:54  brouard
    return( 0 );                         /* we're done */    Summary: times.h is ok with mingw32 now.
 }  
     Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 /******************************************/    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   
 void replace(char *s, char*t)    Revision 1.138  2010/04/30 18:19:40  brouard
 {    *** empty log message ***
   int i;  
   int lg=20;    Revision 1.137  2010/04/29 18:11:38  brouard
   i=0;    (Module): Checking covariates for more complex models
   lg=strlen(t);    than V1+V2. A lot of change to be done. Unstable.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.136  2010/04/26 20:30:53  brouard
     if (t[i]== '\\') s[i]='/';    (Module): merging some libgsl code. Fixing computation
   }    of likelione (using inter/intrapolation if mle = 0) in order to
 }    get same likelihood as if mle=1.
     Some cleaning of code and comments added.
 int nbocc(char *s, char occ)  
 {    Revision 1.135  2009/10/29 15:33:14  brouard
   int i,j=0;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   int lg=20;  
   i=0;    Revision 1.134  2009/10/29 13:18:53  brouard
   lg=strlen(s);    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.133  2009/07/06 10:21:25  brouard
   }    just nforces
   return j;  
 }    Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.131  2009/06/20 16:22:47  brouard
   int i,lg,j,p=0;    Some dimensions resccaled
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.130  2009/05/26 06:44:34  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Module): Max Covariate is now set to 20 instead of 8. A
   }    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.129  2007/08/31 13:49:27  lievre
     (u[j] = t[j]);    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   }  
      u[p]='\0';    Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    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
     loop. Now we define nhstepma in the age loop.
 /********************** nrerror ********************/    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
 void nrerror(char error_text[])    and then all the health expectancies with variances or standard
 {    deviation (needs data from the Hessian matrices) which slows the
   fprintf(stderr,"ERREUR ...\n");    computation.
   fprintf(stderr,"%s\n",error_text);    In the future we should be able to stop the program is only health
   exit(1);    expectancies and graph are needed without standard deviations.
 }  
 /*********************** vector *******************/    Revision 1.126  2006/04/28 17:23:28  brouard
 double *vector(int nl, int nh)    (Module): Yes the sum of survivors was wrong since
 {    imach-114 because nhstepm was no more computed in the age
   double *v;    loop. Now we define nhstepma in the age loop.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Version 0.98h
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.125  2006/04/04 15:20:31  lievre
 }    Errors in calculation of health expectancies. Age was not initialized.
     Forecasting file added.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.124  2006/03/22 17:13:53  lievre
 {    Parameters are printed with %lf instead of %f (more numbers after the comma).
   free((FREE_ARG)(v+nl-NR_END));    The log-likelihood is printed in the log file
 }  
     Revision 1.123  2006/03/20 10:52:43  brouard
 /************************ivector *******************************/    * imach.c (Module): <title> changed, corresponds to .htm file
 int *ivector(long nl,long nh)    name. <head> headers where missing.
 {  
   int *v;    * imach.c (Module): Weights can have a decimal point as for
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    English (a comma might work with a correct LC_NUMERIC environment,
   if (!v) nrerror("allocation failure in ivector");    otherwise the weight is truncated).
   return v-nl+NR_END;    Modification of warning when the covariates values are not 0 or
 }    1.
     Version 0.98g
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.122  2006/03/20 09:45:41  brouard
 {    (Module): Weights can have a decimal point as for
   free((FREE_ARG)(v+nl-NR_END));    English (a comma might work with a correct LC_NUMERIC environment,
 }    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 /******************* imatrix *******************************/    1.
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Version 0.98g
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Revision 1.121  2006/03/16 17:45:01  lievre
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    * imach.c (Module): Comments concerning covariates added
   int **m;  
      * imach.c (Module): refinements in the computation of lli if
   /* allocate pointers to rows */    status=-2 in order to have more reliable computation if stepm is
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    not 1 month. Version 0.98f
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.120  2006/03/16 15:10:38  lievre
   m -= nrl;    (Module): refinements in the computation of lli if
      status=-2 in order to have more reliable computation if stepm is
      not 1 month. Version 0.98f
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.119  2006/03/15 17:42:26  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Bug if status = -2, the loglikelihood was
   m[nrl] += NR_END;    computed as likelihood omitting the logarithm. Version O.98e
   m[nrl] -= ncl;  
      Revision 1.118  2006/03/14 18:20:07  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): varevsij Comments added explaining the second
      table of variances if popbased=1 .
   /* return pointer to array of pointers to rows */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   return m;    (Module): Function pstamp added
 }    (Module): Version 0.98d
   
 /****************** free_imatrix *************************/    Revision 1.117  2006/03/14 17:16:22  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): varevsij Comments added explaining the second
       int **m;    table of variances if popbased=1 .
       long nch,ncl,nrh,nrl;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
      /* free an int matrix allocated by imatrix() */    (Module): Function pstamp added
 {    (Module): Version 0.98d
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.116  2006/03/06 10:29:27  brouard
 }    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.115  2006/02/27 12:17:45  brouard
 {    (Module): One freematrix added in mlikeli! 0.98c
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.114  2006/02/26 12:57:58  brouard
     (Module): Some improvements in processing parameter
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    filename with strsep.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.113  2006/02/24 14:20:24  brouard
   m -= nrl;    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    allocation too.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.112  2006/01/30 09:55:26  brouard
   m[nrl] -= ncl;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.111  2006/01/25 20:38:18  brouard
   return m;    (Module): Lots of cleaning and bugs added (Gompertz)
 }    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Revision 1.110  2006/01/25 00:51:50  brouard
 {    (Module): Lots of cleaning and bugs added (Gompertz)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.109  2006/01/24 19:37:15  brouard
 }    (Module): Comments (lines starting with a #) are allowed in data.
   
 /******************* ma3x *******************************/    Revision 1.108  2006/01/19 18:05:42  lievre
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Gnuplot problem appeared...
 {    To be fixed
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.106  2006/01/19 13:24:36  brouard
   m += NR_END;    Some cleaning and links added in html output
   m -= nrl;  
     Revision 1.105  2006/01/05 20:23:19  lievre
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    *** empty log message ***
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.104  2005/09/30 16:11:43  lievre
   m[nrl] -= ncl;    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    contributions to the likelihood is 1 - Prob of dying from last
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   m[nrl][ncl] += NR_END;    the healthy state at last known wave). Version is 0.98
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.103  2005/09/30 15:54:49  lievre
     m[nrl][j]=m[nrl][j-1]+nlay;    (Module): sump fixed, loop imx fixed, and simplifications.
    
   for (i=nrl+1; i<=nrh; i++) {    Revision 1.102  2004/09/15 17:31:30  brouard
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Add the possibility to read data file including tab characters.
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    Revision 1.101  2004/09/15 10:38:38  brouard
   }    Fix on curr_time
   return m;  
 }    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, 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 ***
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.98  2004/05/16 15:05:56  brouard
   free((FREE_ARG)(m+nrl-NR_END));    New version 0.97 . First attempt to estimate force of mortality
 }    directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
 /***************** f1dim *************************/    This is the basic analysis of mortality and should be done before any
 extern int ncom;    other analysis, in order to test if the mortality estimated from the
 extern double *pcom,*xicom;    cross-longitudinal survey is different from the mortality estimated
 extern double (*nrfunc)(double []);    from other sources like vital statistic data.
    
 double f1dim(double x)    The same imach parameter file can be used but the option for mle should be -3.
 {  
   int j;    Agnès, who wrote this part of the code, tried to keep most of the
   double f;    former routines in order to include the new code within the former code.
   double *xt;  
      The output is very simple: only an estimate of the intercept and of
   xt=vector(1,ncom);    the slope with 95% confident intervals.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    Current limitations:
   free_vector(xt,1,ncom);    A) Even if you enter covariates, i.e. with the
   return f;    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.
   
 /*****************brent *************************/    Revision 1.97  2004/02/20 13:25:42  lievre
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Version 0.96d. Population forecasting command line is (temporarily)
 {    suppressed.
   int iter;  
   double a,b,d,etemp;    Revision 1.96  2003/07/15 15:38:55  brouard
   double fu,fv,fw,fx;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   double ftemp;    rewritten within the same printf. Workaround: many printfs.
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    Revision 1.95  2003/07/08 07:54:34  brouard
      * imach.c (Repository):
   a=(ax < cx ? ax : cx);    (Repository): Using imachwizard code to output a more meaningful covariance
   b=(ax > cx ? ax : cx);    matrix (cov(a12,c31) instead of numbers.
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    Revision 1.94  2003/06/27 13:00:02  brouard
   for (iter=1;iter<=ITMAX;iter++) {    Just cleaning
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    Revision 1.93  2003/06/25 16:33:55  brouard
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    (Module): On windows (cygwin) function asctime_r doesn't
     printf(".");fflush(stdout);    exist so I changed back to asctime which exists.
 #ifdef DEBUG    (Module): Version 0.96b
     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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    Revision 1.92  2003/06/25 16:30:45  brouard
 #endif    (Module): On windows (cygwin) function asctime_r doesn't
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    exist so I changed back to asctime which exists.
       *xmin=x;  
       return fx;    Revision 1.91  2003/06/25 15:30:29  brouard
     }    * imach.c (Repository): Duplicated warning errors corrected.
     ftemp=fu;    (Repository): Elapsed time after each iteration is now output. It
     if (fabs(e) > tol1) {    helps to forecast when convergence will be reached. Elapsed time
       r=(x-w)*(fx-fv);    is stamped in powell.  We created a new html file for the graphs
       q=(x-v)*(fx-fw);    concerning matrix of covariance. It has extension -cov.htm.
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);    Revision 1.90  2003/06/24 12:34:15  brouard
       if (q > 0.0) p = -p;    (Module): Some bugs corrected for windows. Also, when
       q=fabs(q);    mle=-1 a template is output in file "or"mypar.txt with the design
       etemp=e;    of the covariance matrix to be input.
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    Revision 1.89  2003/06/24 12:30:52  brouard
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    (Module): Some bugs corrected for windows. Also, when
       else {    mle=-1 a template is output in file "or"mypar.txt with the design
         d=p/q;    of the covariance matrix to be input.
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)    Revision 1.88  2003/06/23 17:54:56  brouard
           d=SIGN(tol1,xm-x);    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
       }  
     } else {    Revision 1.87  2003/06/18 12:26:01  brouard
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    Version 0.96
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    Revision 1.86  2003/06/17 20:04:08  brouard
     fu=(*f)(u);    (Module): Change position of html and gnuplot routines and added
     if (fu <= fx) {    routine fileappend.
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)    Revision 1.85  2003/06/17 13:12:43  brouard
         SHFT(fv,fw,fx,fu)    * imach.c (Repository): Check when date of death was earlier that
         } else {    current date of interview. It may happen when the death was just
           if (u < x) a=u; else b=u;    prior to the death. In this case, dh was negative and likelihood
           if (fu <= fw || w == x) {    was wrong (infinity). We still send an "Error" but patch by
             v=w;    assuming that the date of death was just one stepm after the
             w=u;    interview.
             fv=fw;    (Repository): Because some people have very long ID (first column)
             fw=fu;    we changed int to long in num[] and we added a new lvector for
           } else if (fu <= fv || v == x || v == w) {    memory allocation. But we also truncated to 8 characters (left
             v=u;    truncation)
             fv=fu;    (Repository): No more line truncation errors.
           }  
         }    Revision 1.84  2003/06/13 21:44:43  brouard
   }    * imach.c (Repository): Replace "freqsummary" at a correct
   nrerror("Too many iterations in brent");    place. It differs from routine "prevalence" which may be called
   *xmin=x;    many times. Probs is memory consuming and must be used with
   return fx;    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 /****************** mnbrak ***********************/    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))    Revision 1.82  2003/06/05 15:57:20  brouard
 {    Add log in  imach.c and  fullversion number is now printed.
   double ulim,u,r,q, dum;  
   double fu;  */
    /*
   *fa=(*func)(*ax);     Interpolated Markov Chain
   *fb=(*func)(*bx);  
   if (*fb > *fa) {    Short summary of the programme:
     SHFT(dum,*ax,*bx,dum)    
       SHFT(dum,*fb,*fa,dum)    This program computes Healthy Life Expectancies from
       }    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   *cx=(*bx)+GOLD*(*bx-*ax);    first survey ("cross") where individuals from different ages are
   *fc=(*func)(*cx);    interviewed on their health status or degree of disability (in the
   while (*fb > *fc) {    case of a health survey which is our main interest) -2- at least a
     r=(*bx-*ax)*(*fb-*fc);    second wave of interviews ("longitudinal") which measure each change
     q=(*bx-*cx)*(*fb-*fa);    (if any) in individual health status.  Health expectancies are
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    computed from the time spent in each health state according to a
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    model. More health states you consider, more time is necessary to reach the
     ulim=(*bx)+GLIMIT*(*cx-*bx);    Maximum Likelihood of the parameters involved in the model.  The
     if ((*bx-u)*(u-*cx) > 0.0) {    simplest model is the multinomial logistic model where pij is the
       fu=(*func)(u);    probability to be observed in state j at the second wave
     } else if ((*cx-u)*(u-ulim) > 0.0) {    conditional to be observed in state i at the first wave. Therefore
       fu=(*func)(u);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       if (fu < *fc) {    'age' is age and 'sex' is a covariate. If you want to have a more
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    complex model than "constant and age", you should modify the program
           SHFT(*fb,*fc,fu,(*func)(u))    where the markup *Covariates have to be included here again* invites
           }    you to do it.  More covariates you add, slower the
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    convergence.
       u=ulim;  
       fu=(*func)(u);    The advantage of this computer programme, compared to a simple
     } else {    multinomial logistic model, is clear when the delay between waves is not
       u=(*cx)+GOLD*(*cx-*bx);    identical for each individual. Also, if a individual missed an
       fu=(*func)(u);    intermediate interview, the information is lost, but taken into
     }    account using an interpolation or extrapolation.  
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)    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
 }    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 /*************** linmin ************************/    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 int ncom;    and the contribution of each individual to the likelihood is simply
 double *pcom,*xicom;    hPijx.
 double (*nrfunc)(double []);  
      Also this programme outputs the covariance matrix of the parameters but also
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    of the life expectancies. It also computes the period (stable) prevalence. 
 {    
   double brent(double ax, double bx, double cx,    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
                double (*f)(double), double tol, double *xmin);             Institut national d'études démographiques, Paris.
   double f1dim(double x);    This software have been partly granted by Euro-REVES, a concerted action
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    from the European Union.
               double *fc, double (*func)(double));    It is copyrighted identically to a GNU software product, ie programme and
   int j;    software can be distributed freely for non commercial use. Latest version
   double xx,xmin,bx,ax;    can be accessed at http://euroreves.ined.fr/imach .
   double fx,fb,fa;  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   ncom=n;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   pcom=vector(1,n);    
   xicom=vector(1,n);    **********************************************************************/
   nrfunc=func;  /*
   for (j=1;j<=n;j++) {    main
     pcom[j]=p[j];    read parameterfile
     xicom[j]=xi[j];    read datafile
   }    concatwav
   ax=0.0;    freqsummary
   xx=1.0;    if (mle >= 1)
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      mlikeli
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    print results files
 #ifdef DEBUG    if mle==1 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);       computes hessian
 #endif    read end of parameter file: agemin, agemax, bage, fage, estepm
   for (j=1;j<=n;j++) {        begin-prev-date,...
     xi[j] *= xmin;    open gnuplot file
     p[j] += xi[j];    open html file
   }    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   free_vector(xicom,1,n);     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   free_vector(pcom,1,n);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 }      freexexit2 possible for memory heap.
   
 /*************** powell ************************/    h Pij x                         | pij_nom  ficrestpij
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
             double (*func)(double []))         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
 {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   int i,ibig,j;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   double del,t,*pt,*ptt,*xit;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   double fp,fptt;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   double *xits;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   pt=vector(1,n);  
   ptt=vector(1,n);    forecasting if prevfcast==1 prevforecast call prevalence()
   xit=vector(1,n);    health expectancies
   xits=vector(1,n);    Variance-covariance of DFLE
   *fret=(*func)(p);    prevalence()
   for (j=1;j<=n;j++) pt[j]=p[j];     movingaverage()
   for (*iter=1;;++(*iter)) {    varevsij() 
     fp=(*fret);    if popbased==1 varevsij(,popbased)
     ibig=0;    total life expectancies
     del=0.0;    Variance of period (stable) prevalence
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);   end
     for (i=1;i<=n;i++)  */
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  /* #define DEBUG */
     for (i=1;i<=n;i++) {  /* #define DEBUGBRENT */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #define POWELL /* Instead of NLOPT */
       fptt=(*fret);  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
 #ifdef DEBUG  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
       printf("fret=%lf \n",*fret);  
 #endif  #include <math.h>
       printf("%d",i);fflush(stdout);  #include <stdio.h>
       linmin(p,xit,n,fret,func);  #include <stdlib.h>
       if (fabs(fptt-(*fret)) > del) {  #include <string.h>
         del=fabs(fptt-(*fret));  
         ibig=i;  #ifdef _WIN32
       }  #include <io.h>
 #ifdef DEBUG  #include <windows.h>
       printf("%d %.12e",i,(*fret));  #include <tchar.h>
       for (j=1;j<=n;j++) {  #else
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #include <unistd.h>
         printf(" x(%d)=%.12e",j,xit[j]);  #endif
       }  
       for(j=1;j<=n;j++)  #include <limits.h>
         printf(" p=%.12e",p[j]);  #include <sys/types.h>
       printf("\n");  
 #endif  #if defined(__GNUC__)
     }  #include <sys/utsname.h> /* Doesn't work on Windows */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #endif
 #ifdef DEBUG  
       int k[2],l;  #include <sys/stat.h>
       k[0]=1;  #include <errno.h>
       k[1]=-1;  /* extern int errno; */
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  /* #ifdef LINUX */
         printf(" %.12e",p[j]);  /* #include <time.h> */
       printf("\n");  /* #include "timeval.h" */
       for(l=0;l<=1;l++) {  /* #else */
         for (j=1;j<=n;j++) {  /* #include <sys/time.h> */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /* #endif */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  #include <time.h>
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  #ifdef GSL
 #endif  #include <gsl/gsl_errno.h>
   #include <gsl/gsl_multimin.h>
   #endif
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  #ifdef NLOPT
       free_vector(pt,1,n);  #include <nlopt.h>
       return;  typedef struct {
     }    double (* function)(double [] );
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  } myfunc_data ;
     for (j=1;j<=n;j++) {  #endif
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  /* #include <libintl.h> */
       pt[j]=p[j];  /* #define _(String) gettext (String) */
     }  
     fptt=(*func)(ptt);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define GNUPLOTPROGRAM "gnuplot"
       if (t < 0.0) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         linmin(p,xit,n,fret,func);  #define FILENAMELENGTH 132
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
           xi[j][n]=xit[j];  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
         }  
 #ifdef DEBUG  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  #define NINTERVMAX 8
         printf("\n");  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #endif  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       }  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
     }  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   }  #define MAXN 20000
 }  #define YEARM 12. /**< Number of months per year */
   #define AGESUP 130
 /**** Prevalence limit ****************/  #define AGEBASE 40
   #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #ifdef _WIN32
 {  #define DIRSEPARATOR '\\'
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #define CHARSEPARATOR "\\"
      matrix by transitions matrix until convergence is reached */  #define ODIRSEPARATOR '/'
   #else
   int i, ii,j,k;  #define DIRSEPARATOR '/'
   double min, max, maxmin, maxmax,sumnew=0.;  #define CHARSEPARATOR "/"
   double **matprod2();  #define ODIRSEPARATOR '\\'
   double **out, cov[NCOVMAX], **pmij();  #endif
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  /* $Id$ */
   /* $State$ */
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char fullversion[]="$Revision$ $Date$"; 
     }  char strstart[80];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH];
    cov[1]=1.;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     newm=savm;  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     /* Covariates have to be included here again */  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
      cov[2]=agefin;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
    int cptcovprodnoage=0; /**< Number of covariate products without age */   
       for (k=1; k<=cptcovn;k++) {  int cptcoveff=0; /* Total number of covariates to vary for printing results */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int cptcov=0; /* Working variable */
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  int npar=NPARMAX;
       }  int nlstate=2; /* Number of live states */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int ndeath=1; /* Number of dead states */
       for (k=1; k<=cptcovprod;k++)  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  int popbased=0;
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int *wav; /* Number of waves for this individuual 0 is possible */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  int maxwav=0; /* Maxim number of waves */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     savm=oldm;                     to the likelihood and the sum of weights (done by funcone)*/
     oldm=newm;  int mle=1, weightopt=0;
     maxmax=0.;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     for(j=1;j<=nlstate;j++){  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       min=1.;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       max=0.;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       for(i=1; i<=nlstate; i++) {  int countcallfunc=0;  /* Count the number of calls to func */
         sumnew=0;  double jmean=1; /* Mean space between 2 waves */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double **matprod2(); /* test */
         prlim[i][j]= newm[i][j]/(1-sumnew);  double **oldm, **newm, **savm; /* Working pointers to matrices */
         max=FMAX(max,prlim[i][j]);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
         min=FMIN(min,prlim[i][j]);  /*FILE *fic ; */ /* Used in readdata only */
       }  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       maxmin=max-min;  FILE *ficlog, *ficrespow;
       maxmax=FMAX(maxmax,maxmin);  int globpr=0; /* Global variable for printing or not */
     }  double fretone; /* Only one call to likelihood */
     if(maxmax < ftolpl){  long ipmx=0; /* Number of contributions */
       return prlim;  double sw; /* Sum of weights */
     }  char filerespow[FILENAMELENGTH];
   }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 }  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 /*************** transition probabilities ***************/  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   double s1, s2;  FILE *ficresstdeij;
   /*double t34;*/  char fileresstde[FILENAMELENGTH];
   int i,j,j1, nc, ii, jj;  FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
     for(i=1; i<= nlstate; i++){  FILE  *ficresvij;
     for(j=1; j<i;j++){  char fileresv[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  FILE  *ficresvpl;
         /*s2 += param[i][j][nc]*cov[nc];*/  char fileresvpl[FILENAMELENGTH];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char title[MAXLINE];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       ps[i][j]=s2;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char command[FILENAMELENGTH];
     }  int  outcmd=0;
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
       ps[i][j]=s2;  char fileregp[FILENAMELENGTH];
     }  char popfile[FILENAMELENGTH];
   }  
     /*ps[3][2]=1;*/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
   for(i=1; i<= nlstate; i++){  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
      s1=0;  /* struct timezone tzp; */
     for(j=1; j<i; j++)  /* extern int gettimeofday(); */
       s1+=exp(ps[i][j]);  struct tm tml, *gmtime(), *localtime();
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  extern time_t time();
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     for(j=i+1; j<=nlstate+ndeath; j++)  struct tm tm;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  char strcurr[80], strfor[80];
   } /* end i */  
   char *endptr;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  long lval;
     for(jj=1; jj<= nlstate+ndeath; jj++){  double dval;
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  #define NR_END 1
     }  #define FREE_ARG char*
   }  #define FTOL 1.0e-10
   
   #define NRANSI 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #define ITMAX 200 
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  #define TOL 2.0e-4 
    }  
     printf("\n ");  #define CGOLD 0.3819660 
     }  #define ZEPS 1.0e-10 
     printf("\n ");printf("%lf ",cov[2]);*/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  #define GOLD 1.618034 
   goto end;*/  #define GLIMIT 100.0 
     return ps;  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 /**************** Product of 2 matrices ******************/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  #define rint(a) floor(a+0.5)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
   /* in, b, out are matrice of pointers which should have been initialized  #define mytinydouble 1.0e-16
      before: only the contents of out is modified. The function returns  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
      a pointer to pointers identical to out */  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   long i, j, k;  /* static double dsqrarg; */
   for(i=nrl; i<= nrh; i++)  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
     for(k=ncolol; k<=ncoloh; k++)  static double sqrarg;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         out[i][k] +=in[i][j]*b[j][k];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
   return out;  
 }  int imx; 
   int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
 /************* Higher Matrix Product ***************/  
   int estepm;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  int m,nb;
      duration (i.e. until  long *num;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
      (typically every 2 years instead of every month which is too big).  double **pmmij, ***probs;
      Model is determined by parameters x and covariates have to be  double *ageexmed,*agecens;
      included manually here.  double dateintmean=0;
   
      */  double *weight;
   int **s; /* Status */
   int i, j, d, h, k;  double *agedc;
   double **out, cov[NCOVMAX];  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   double **newm;                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
   /* Hstepm could be zero and should return the unit matrix */  double  idx; 
   for (i=1;i<=nlstate+ndeath;i++)  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
     for (j=1;j<=nlstate+ndeath;j++){  int *Ndum; /** Freq of modality (tricode */
       oldm[i][j]=(i==j ? 1.0 : 0.0);  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     }  double *lsurv, *lpop, *tpop;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
     for(d=1; d <=hstepm; d++){  double ftolhess; /**< Tolerance for computing hessian */
       newm=savm;  
       /* Covariates have to be included here again */  /**************** split *************************/
       cov[1]=1.;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       for (k=1; k<=cptcovage;k++)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    */ 
       for (k=1; k<=cptcovprod;k++)    char  *ss;                            /* pointer */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    int   l1=0, l2=0;                             /* length counters */
   
     l1 = strlen(path );                   /* length of path */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    if ( ss == NULL ) {                   /* no directory, so determine current directory */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      strcpy( name, path );               /* we got the fullname name because no directory */
       savm=oldm;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       oldm=newm;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     }      /* get current working directory */
     for(i=1; i<=nlstate+ndeath; i++)      /*    extern  char* getcwd ( char *buf , int len);*/
       for(j=1;j<=nlstate+ndeath;j++) {  #ifdef WIN32
         po[i][j][h]=newm[i][j];      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  #else
          */          if (getcwd(dirc, FILENAME_MAX) == NULL) {
       }  #endif
   } /* end h */        return( GLOCK_ERROR_GETCWD );
   return po;      }
 }      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
 /*************** log-likelihood *************/      ss++;                               /* after this, the filename */
 double func( double *x)      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i, ii, j, k, mi, d, kk;      strcpy( name, ss );         /* save file name */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   double **out;      dirc[l1-l2] = '\0';                 /* add zero */
   double sw; /* Sum of weights */      printf(" DIRC2 = %s \n",dirc);
   double lli; /* Individual log likelihood */    }
   long ipmx;    /* We add a separator at the end of dirc if not exists */
   /*extern weight */    l1 = strlen( dirc );                  /* length of directory */
   /* We are differentiating ll according to initial status */    if( dirc[l1-1] != DIRSEPARATOR ){
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      dirc[l1] =  DIRSEPARATOR;
   /*for(i=1;i<imx;i++)      dirc[l1+1] = 0; 
     printf(" %d\n",s[4][i]);      printf(" DIRC3 = %s \n",dirc);
   */    }
   cov[1]=1.;    ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
   for(k=1; k<=nlstate; k++) ll[k]=0.;      ss++;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      strcpy(ext,ss);                     /* save extension */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      l1= strlen( name);
     for(mi=1; mi<= wav[i]-1; mi++){      l2= strlen(ss)+1;
       for (ii=1;ii<=nlstate+ndeath;ii++)      strncpy( finame, name, l1-l2);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      finame[l1-l2]= 0;
       for(d=0; d<dh[mi][i]; d++){    }
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return( 0 );                          /* we're done */
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  
          /******************************************/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  void replace_back_to_slash(char *s, char*t)
         savm=oldm;  {
         oldm=newm;    int i;
            int lg=0;
            i=0;
       } /* end mult */    lg=strlen(t);
          for(i=0; i<= lg; i++) {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      (s[i] = t[i]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      if (t[i]== '\\') s[i]='/';
       ipmx +=1;    }
       sw += weight[i];  }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  char *trimbb(char *out, char *in)
   } /* end of individual */  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     char *s;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    s=out;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    while (*in != '\0'){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   return -l;        in++;
 }      }
       *out++ = *in++;
     }
 /*********** Maximum Likelihood Estimation ***************/    *out='\0';
     return s;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  }
 {  
   int i,j, iter;  /* char *substrchaine(char *out, char *in, char *chain) */
   double **xi,*delti;  /* { */
   double fret;  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
   xi=matrix(1,npar,1,npar);  /*   char *s, *t; */
   for (i=1;i<=npar;i++)  /*   t=in;s=out; */
     for (j=1;j<=npar;j++)  /*   while ((*in != *chain) && (*in != '\0')){ */
       xi[i][j]=(i==j ? 1.0 : 0.0);  /*     *out++ = *in++; */
   printf("Powell\n");  /*   } */
   powell(p,xi,npar,ftol,&iter,&fret,func);  
   /*   /\* *in matches *chain *\/ */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  /*   while ((*in++ == *chain++) && (*in != '\0')){ */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*   } */
 }  /*   in--; chain--; */
   /*   while ( (*in != '\0')){ */
 /**** Computes Hessian and covariance matrix ***/  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*     *out++ = *in++; */
 {  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   double  **a,**y,*x,pd;  /*   } */
   double **hess;  /*   *out='\0'; */
   int i, j,jk;  /*   out=s; */
   int *indx;  /*   return out; */
   /* } */
   double hessii(double p[], double delta, int theta, double delti[]);  char *substrchaine(char *out, char *in, char *chain)
   double hessij(double p[], double delti[], int i, int j);  {
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /* Substract chain 'chain' from 'in', return and output 'out' */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    /* in="V1+V1*age+age*age+V2", chain="age*age" */
   
   hess=matrix(1,npar,1,npar);    char *strloc;
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    strcpy (out, in); 
   for (i=1;i<=npar;i++){    strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
     printf("%d",i);fflush(stdout);    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
     hess[i][i]=hessii(p,ftolhess,i,delti);    if(strloc != NULL){ 
     /*printf(" %f ",p[i]);*/      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
     /*printf(" %lf ",hess[i][i]);*/      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
   }      /* strcpy (strloc, strloc +strlen(chain));*/
      }
   for (i=1;i<=npar;i++) {    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
     for (j=1;j<=npar;j++)  {    return out;
       if (j>i) {  }
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      char *cutl(char *blocc, char *alocc, char *in, char occ)
         /*printf(" %lf ",hess[i][j]);*/  {
       }    /* 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')
   }       gives blocc="abcdef" and alocc="ghi2j".
   printf("\n");       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    char *s, *t;
      t=in;s=in;
   a=matrix(1,npar,1,npar);    while ((*in != occ) && (*in != '\0')){
   y=matrix(1,npar,1,npar);      *alocc++ = *in++;
   x=vector(1,npar);    }
   indx=ivector(1,npar);    if( *in == occ){
   for (i=1;i<=npar;i++)      *(alocc)='\0';
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      s=++in;
   ludcmp(a,npar,indx,&pd);    }
    
   for (j=1;j<=npar;j++) {    if (s == t) {/* occ not found */
     for (i=1;i<=npar;i++) x[i]=0;      *(alocc-(in-s))='\0';
     x[j]=1;      in=s;
     lubksb(a,npar,indx,x);    }
     for (i=1;i<=npar;i++){    while ( *in != '\0'){
       matcov[i][j]=x[i];      *blocc++ = *in++;
     }    }
   }  
     *blocc='\0';
   printf("\n#Hessian matrix#\n");    return t;
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++) {  char *cutv(char *blocc, char *alocc, char *in, char occ)
       printf("%.3e ",hess[i][j]);  {
     }    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
     printf("\n");       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   }       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
   /* Recompute Inverse */    */
   for (i=1;i<=npar;i++)    char *s, *t;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    t=in;s=in;
   ludcmp(a,npar,indx,&pd);    while (*in != '\0'){
       while( *in == occ){
   /*  printf("\n#Hessian matrix recomputed#\n");        *blocc++ = *in++;
         s=in;
   for (j=1;j<=npar;j++) {      }
     for (i=1;i<=npar;i++) x[i]=0;      *blocc++ = *in++;
     x[j]=1;    }
     lubksb(a,npar,indx,x);    if (s == t) /* occ not found */
     for (i=1;i<=npar;i++){      *(blocc-(in-s))='\0';
       y[i][j]=x[i];    else
       printf("%.3e ",y[i][j]);      *(blocc-(in-s)-1)='\0';
     }    in=s;
     printf("\n");    while ( *in != '\0'){
   }      *alocc++ = *in++;
   */    }
   
   free_matrix(a,1,npar,1,npar);    *alocc='\0';
   free_matrix(y,1,npar,1,npar);    return s;
   free_vector(x,1,npar);  }
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  int nbocc(char *s, char occ)
   {
     int i,j=0;
 }    int lg=20;
     i=0;
 /*************** hessian matrix ****************/    lg=strlen(s);
 double hessii( double x[], double delta, int theta, double delti[])    for(i=0; i<= lg; i++) {
 {    if  (s[i] == occ ) j++;
   int i;    }
   int l=1, lmax=20;    return j;
   double k1,k2;  }
   double p2[NPARMAX+1];  
   double res;  /* void cutv(char *u,char *v, char*t, char occ) */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /* { */
   double fx;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   int k=0,kmax=10;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   double l1;  /*      gives u="abcdef2ghi" and v="j" *\/ */
   /*   int i,lg,j,p=0; */
   fx=func(x);  /*   i=0; */
   for (i=1;i<=npar;i++) p2[i]=x[i];  /*   lg=strlen(t); */
   for(l=0 ; l <=lmax; l++){  /*   for(j=0; j<=lg-1; j++) { */
     l1=pow(10,l);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     delts=delt;  /*   } */
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  /*   for(j=0; j<p; j++) { */
       p2[theta]=x[theta] +delt;  /*     (u[j] = t[j]); */
       k1=func(p2)-fx;  /*   } */
       p2[theta]=x[theta]-delt;  /*      u[p]='\0'; */
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */  /*    for(j=0; j<= lg; j++) { */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
        /*   } */
 #ifdef DEBUG  /* } */
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif  #ifdef _WIN32
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  char * strsep(char **pp, const char *delim)
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  {
         k=kmax;    char *p, *q;
       }           
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    if ((p = *pp) == NULL)
         k=kmax; l=lmax*10.;      return 0;
       }    if ((q = strpbrk (p, delim)) != NULL)
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    {
         delts=delt;      *pp = q + 1;
       }      *q = '\0';
     }    }
   }    else
   delti[theta]=delts;      *pp = 0;
   return res;    return p;
    }
 }  #endif
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  /********************** nrerror ********************/
 {  
   int i;  void nrerror(char error_text[])
   int l=1, l1, lmax=20;  {
   double k1,k2,k3,k4,res,fx;    fprintf(stderr,"ERREUR ...\n");
   double p2[NPARMAX+1];    fprintf(stderr,"%s\n",error_text);
   int k;    exit(EXIT_FAILURE);
   }
   fx=func(x);  /*********************** vector *******************/
   for (k=1; k<=2; k++) {  double *vector(int nl, int nh)
     for (i=1;i<=npar;i++) p2[i]=x[i];  {
     p2[thetai]=x[thetai]+delti[thetai]/k;    double *v;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     k1=func(p2)-fx;    if (!v) nrerror("allocation failure in vector");
      return v-nl+NR_END;
     p2[thetai]=x[thetai]+delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  /************************ free vector ******************/
    void free_vector(double*v, int nl, int nh)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    free((FREE_ARG)(v+nl-NR_END));
     k3=func(p2)-fx;  }
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /************************ivector *******************************/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  int *ivector(long nl,long nh)
     k4=func(p2)-fx;  {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    int *v;
 #ifdef DEBUG    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     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 (!v) nrerror("allocation failure in ivector");
 #endif    return v-nl+NR_END;
   }  }
   return res;  
 }  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
 /************** Inverse of matrix **************/  {
 void ludcmp(double **a, int n, int *indx, double *d)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   int i,imax,j,k;  
   double big,dum,sum,temp;  /************************lvector *******************************/
   double *vv;  long *lvector(long nl,long nh)
    {
   vv=vector(1,n);    long *v;
   *d=1.0;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   for (i=1;i<=n;i++) {    if (!v) nrerror("allocation failure in ivector");
     big=0.0;    return v-nl+NR_END;
     for (j=1;j<=n;j++)  }
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  /******************free lvector **************************/
     vv[i]=1.0/big;  void free_lvector(long *v, long nl, long nh)
   }  {
   for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
     for (i=1;i<j;i++) {  }
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  /******************* imatrix *******************************/
       a[i][j]=sum;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     big=0.0;  { 
     for (i=j;i<=n;i++) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       sum=a[i][j];    int **m; 
       for (k=1;k<j;k++)    
         sum -= a[i][k]*a[k][j];    /* allocate pointers to rows */ 
       a[i][j]=sum;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       if ( (dum=vv[i]*fabs(sum)) >= big) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
         big=dum;    m += NR_END; 
         imax=i;    m -= nrl; 
       }    
     }    
     if (j != imax) {    /* allocate rows and set pointers to them */ 
       for (k=1;k<=n;k++) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         dum=a[imax][k];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         a[imax][k]=a[j][k];    m[nrl] += NR_END; 
         a[j][k]=dum;    m[nrl] -= ncl; 
       }    
       *d = -(*d);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       vv[imax]=vv[j];    
     }    /* return pointer to array of pointers to rows */ 
     indx[j]=imax;    return m; 
     if (a[j][j] == 0.0) a[j][j]=TINY;  } 
     if (j != n) {  
       dum=1.0/(a[j][j]);  /****************** free_imatrix *************************/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  void free_imatrix(m,nrl,nrh,ncl,nch)
     }        int **m;
   }        long nch,ncl,nrh,nrl; 
   free_vector(vv,1,n);  /* Doesn't work */       /* free an int matrix allocated by imatrix() */ 
 ;  { 
 }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
 void lubksb(double **a, int n, int *indx, double b[])  } 
 {  
   int i,ii=0,ip,j;  /******************* matrix *******************************/
   double sum;  double **matrix(long nrl, long nrh, long ncl, long nch)
    {
   for (i=1;i<=n;i++) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     ip=indx[i];    double **m;
     sum=b[ip];  
     b[ip]=b[i];    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (ii)    if (!m) nrerror("allocation failure 1 in matrix()");
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    m += NR_END;
     else if (sum) ii=i;    m -= nrl;
     b[i]=sum;  
   }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (i=n;i>=1;i--) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     sum=b[i];    m[nrl] += NR_END;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    m[nrl] -= ncl;
     b[i]=sum/a[i][i];  
   }    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])
 /************ Frequencies ********************/  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
 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)  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
 {  /* Some frequencies */     */
    }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  /*************************free matrix ************************/
   double *pp;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double pos, k2, dateintsum=0,k2cpt=0;  {
   FILE *ficresp;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   char fileresp[FILENAMELENGTH];    free((FREE_ARG)(m+nrl-NR_END));
    }
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /******************* ma3x *******************************/
   strcpy(fileresp,"p");  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   strcat(fileresp,fileres);  {
   if((ficresp=fopen(fileresp,"w"))==NULL) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double ***m;
     exit(0);  
   }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    if (!m) nrerror("allocation failure 1 in matrix()");
   j1=0;    m += NR_END;
      m -= nrl;
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for(k1=1; k1<=j;k1++){    m[nrl] += NR_END;
     for(i1=1; i1<=ncodemax[k1];i1++){    m[nrl] -= ncl;
       j1++;  
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)      m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         for (jk=-1; jk<=nlstate+ndeath; jk++)      if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
           for(m=agemin; m <= agemax+3; m++)    m[nrl][ncl] += NR_END;
             freq[i][jk][m]=0;    m[nrl][ncl] -= nll;
          for (j=ncl+1; j<=nch; j++) 
       dateintsum=0;      m[nrl][j]=m[nrl][j-1]+nlay;
       k2cpt=0;    
       for (i=1; i<=imx; i++) {    for (i=nrl+1; i<=nrh; i++) {
         bool=1;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         if  (cptcovn>0) {      for (j=ncl+1; j<=nch; j++) 
           for (z1=1; z1<=cptcoveff; z1++)        m[i][j]=m[i][j-1]+nlay;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    }
               bool=0;    return m; 
         }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         if (bool==1) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
           for(m=firstpass; m<=lastpass; m++){    */
             k2=anint[m][i]+(mint[m][i]/12.);  }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;  /*************************free ma3x ************************/
               if(agev[m][i]==1) agev[m][i]=agemax+2;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
               if (m<lastpass) {  {
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
               }    free((FREE_ARG)(m+nrl-NR_END));
                }
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  
                 dateintsum=dateintsum+k2;  /*************** function subdirf ***********/
                 k2cpt++;  char *subdirf(char fileres[])
               }  {
             }    /* Caution optionfilefiname is hidden */
           }    strcpy(tmpout,optionfilefiname);
         }    strcat(tmpout,"/"); /* Add to the right */
       }    strcat(tmpout,fileres);
            return tmpout;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  }
   
       if  (cptcovn>0) {  /*************** function subdirf2 ***********/
         fprintf(ficresp, "\n#********** Variable ");  char *subdirf2(char fileres[], char *preop)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  {
         fprintf(ficresp, "**********\n#");    
       }    /* Caution optionfilefiname is hidden */
       for(i=1; i<=nlstate;i++)    strcpy(tmpout,optionfilefiname);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    strcat(tmpout,"/");
       fprintf(ficresp, "\n");    strcat(tmpout,preop);
          strcat(tmpout,fileres);
       for(i=(int)agemin; i <= (int)agemax+3; i++){    return tmpout;
         if(i==(int)agemax+3)  }
           printf("Total");  
         else  /*************** function subdirf3 ***********/
           printf("Age %d", i);  char *subdirf3(char fileres[], char *preop, char *preop2)
         for(jk=1; jk <=nlstate ; jk++){  {
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    
             pp[jk] += freq[jk][m][i];    /* Caution optionfilefiname is hidden */
         }    strcpy(tmpout,optionfilefiname);
         for(jk=1; jk <=nlstate ; jk++){    strcat(tmpout,"/");
           for(m=-1, pos=0; m <=0 ; m++)    strcat(tmpout,preop);
             pos += freq[jk][m][i];    strcat(tmpout,preop2);
           if(pp[jk]>=1.e-10)    strcat(tmpout,fileres);
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    return tmpout;
           else  }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
         }  char *asc_diff_time(long time_sec, char ascdiff[])
   {
         for(jk=1; jk <=nlstate ; jk++){    long sec_left, days, hours, minutes;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    days = (time_sec) / (60*60*24);
             pp[jk] += freq[jk][m][i];    sec_left = (time_sec) % (60*60*24);
         }    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
         for(jk=1,pos=0; jk <=nlstate ; jk++)    minutes = (sec_left) /60;
           pos += pp[jk];    sec_left = (sec_left) % (60);
         for(jk=1; jk <=nlstate ; jk++){    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
           if(pos>=1.e-5)    return ascdiff;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  }
           else  
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  /***************** f1dim *************************/
           if( i <= (int) agemax){  extern int ncom; 
             if(pos>=1.e-5){  extern double *pcom,*xicom;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  extern double (*nrfunc)(double []); 
               probs[i][jk][j1]= pp[jk]/pos;   
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  double f1dim(double x) 
             }  { 
             else    int j; 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    double f;
           }    double *xt; 
         }   
            xt=vector(1,ncom); 
         for(jk=-1; jk <=nlstate+ndeath; jk++)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
           for(m=-1; m <=nlstate+ndeath; m++)    f=(*nrfunc)(xt); 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    free_vector(xt,1,ncom); 
         if(i <= (int) agemax)    return f; 
           fprintf(ficresp,"\n");  } 
         printf("\n");  
       }  /*****************brent *************************/
     }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   }  {
   dateintmean=dateintsum/k2cpt;    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
       * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
   fclose(ficresp);     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
   free_vector(pp,1,nlstate);     * returned function value. 
      */
   /* End of Freq */    int iter; 
 }    double a,b,d,etemp;
     double fu=0,fv,fw,fx;
 /************ Prevalence ********************/    double ftemp=0.;
 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)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 {  /* Some frequencies */    double e=0.0; 
     
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    a=(ax < cx ? ax : cx); 
   double ***freq; /* Frequencies */    b=(ax > cx ? ax : cx); 
   double *pp;    x=w=v=bx; 
   double pos, k2;    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
   pp=vector(1,nlstate);      xm=0.5*(a+b); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
        /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      printf(".");fflush(stdout);
   j1=0;      fprintf(ficlog,".");fflush(ficlog);
    #ifdef DEBUGBRENT
   j=cptcoveff;      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);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
        /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   for(k1=1; k1<=j;k1++){  #endif
     for(i1=1; i1<=ncodemax[k1];i1++){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       j1++;        *xmin=x; 
              return fx; 
       for (i=-1; i<=nlstate+ndeath; i++)        } 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        ftemp=fu;
           for(m=agemin; m <= agemax+3; m++)      if (fabs(e) > tol1) { 
             freq[i][jk][m]=0;        r=(x-w)*(fx-fv); 
              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) {        } 
                 if (calagedate>0)      } else { 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                 else      } 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      fu=(*f)(u); 
               }      if (fu <= fx) { 
             }        if (u >= x) a=x; else b=x; 
           }        SHFT(v,w,x,u) 
         }        SHFT(fv,fw,fx,fu) 
       }      } else { 
       for(i=(int)agemin; i <= (int)agemax+3; i++){        if (u < x) a=u; else b=u; 
         for(jk=1; jk <=nlstate ; jk++){        if (fu <= fw || w == x) { 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          v=w; 
             pp[jk] += freq[jk][m][i];          w=u; 
         }          fv=fw; 
         for(jk=1; jk <=nlstate ; jk++){          fw=fu; 
           for(m=-1, pos=0; m <=0 ; m++)        } else if (fu <= fv || v == x || v == w) { 
             pos += freq[jk][m][i];          v=u; 
         }          fv=fu; 
                } 
         for(jk=1; jk <=nlstate ; jk++){      } 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    } 
             pp[jk] += freq[jk][m][i];    nrerror("Too many iterations in brent"); 
         }    *xmin=x; 
            return fx; 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  } 
          
         for(jk=1; jk <=nlstate ; jk++){      /****************** mnbrak ***********************/
           if( i <= (int) agemax){  
             if(pos>=1.e-5){  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               probs[i][jk][j1]= pp[jk]/pos;              double (*func)(double)) 
             }  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
           }  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
          values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
       }     */
     }    double ulim,u,r,q, dum;
   }    double fu; 
   
      double scale=10.;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    int iterscale=0;
   free_vector(pp,1,nlstate);  
      *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
 }  /* End of Freq */    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
   
 /************* Waves Concatenation ***************/  
     /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
 {    /*   *bx = *ax - (*ax - *bx)/scale; */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
      Death is a valid wave (if date is known).    /* } */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    if (*fb > *fa) { 
      and mw[mi+1][i]. dh depends on stepm.      SHFT(dum,*ax,*bx,dum) 
      */      SHFT(dum,*fb,*fa,dum) 
     } 
   int i, mi, m;    *cx=(*bx)+GOLD*(*bx-*ax); 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    *fc=(*func)(*cx); 
      double sum=0., jmean=0.;*/  #ifdef DEBUG
     printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
   int j, k=0,jk, ju, jl;    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
   double sum=0.;  #endif
   jmin=1e+5;    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
   jmax=-1;      r=(*bx-*ax)*(*fb-*fc); 
   jmean=0.;      q=(*bx-*cx)*(*fb-*fa); 
   for(i=1; i<=imx; i++){      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     mi=0;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
     m=firstpass;      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
     while(s[m][i] <= nlstate){      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
       if(s[m][i]>=1)        fu=(*func)(u); 
         mw[++mi][i]=m;  #ifdef DEBUG
       if(m >=lastpass)        /* f(x)=A(x-u)**2+f(u) */
         break;        double A, fparabu; 
       else        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         m++;        fparabu= *fa - A*(*ax-u)*(*ax-u);
     }/* end while */        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);
     if (s[m][i] > nlstate){        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);
       mi++;     /* Death is another wave */        /* And thus,it can be that fu > *fc even if fparabu < *fc */
       /* if(mi==0)  never been interviewed correctly before death */        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
          /* Only death is a correct wave */          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
       mw[mi][i]=m;        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
     }  #endif 
   #ifdef MNBRAKORIGINAL
     wav[i]=mi;  #else
     if(mi==0)        if (fu > *fc) {
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  #ifdef DEBUG
   }        printf("mnbrak4  fu > fc \n");
         fprintf(ficlog, "mnbrak4 fu > fc\n");
   for(i=1; i<=imx; i++){  #endif
     for(mi=1; mi<wav[i];mi++){          /* 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 *\/  */
       if (stepm <=0)          /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
         dh[mi][i]=1;          dum=u; /* Shifting c and u */
       else{          u = *cx;
         if (s[mw[mi+1][i]][i] > nlstate) {          *cx = dum;
           if (agedc[i] < 2*AGESUP) {          dum = fu;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          fu = *fc;
           if(j==0) j=1;  /* Survives at least one month after exam */          *fc =dum;
           k=k+1;        } else { /* end */
           if (j >= jmax) jmax=j;  #ifdef DEBUG
           if (j <= jmin) jmin=j;        printf("mnbrak3  fu < fc \n");
           sum=sum+j;        fprintf(ficlog, "mnbrak3 fu < fc\n");
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  #endif
           }          dum=u; /* Shifting c and u */
         }          u = *cx;
         else{          *cx = dum;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          dum = fu;
           k=k+1;          fu = *fc;
           if (j >= jmax) jmax=j;          *fc =dum;
           else if (j <= jmin)jmin=j;        }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  #endif
           sum=sum+j;      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
         }  #ifdef DEBUG
         jk= j/stepm;        printf("mnbrak2  u after c but before ulim\n");
         jl= j -jk*stepm;        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
         ju= j -(jk+1)*stepm;  #endif
         if(jl <= -ju)        fu=(*func)(u); 
           dh[mi][i]=jk;        if (fu < *fc) { 
         else  #ifdef DEBUG
           dh[mi][i]=jk+1;        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
         if(dh[mi][i]==0)        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
           dh[mi][i]=1; /* At least one step */  #endif
       }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     }          SHFT(*fb,*fc,fu,(*func)(u)) 
   }        } 
   jmean=sum/k;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  #ifdef DEBUG
  }        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
 /*********** Tricode ****************************/        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
 void tricode(int *Tvar, int **nbcode, int imx)  #endif
 {        u=ulim; 
   int Ndum[20],ij=1, k, j, i;        fu=(*func)(u); 
   int cptcode=0;      } else { /* u could be left to b (if r > q parabola has a maximum) */
   cptcoveff=0;  #ifdef DEBUG
          printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
   for (k=0; k<19; k++) Ndum[k]=0;        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
   for (k=1; k<=7; k++) ncodemax[k]=0;  #endif
         u=(*cx)+GOLD*(*cx-*bx); 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        fu=(*func)(u); 
     for (i=1; i<=imx; i++) {      } /* end tests */
       ij=(int)(covar[Tvar[j]][i]);      SHFT(*ax,*bx,*cx,u) 
       Ndum[ij]++;      SHFT(*fa,*fb,*fc,fu) 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  #ifdef DEBUG
       if (ij > cptcode) cptcode=ij;        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);
     }        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);
   #endif
     for (i=0; i<=cptcode; i++) {    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
       if(Ndum[i]!=0) ncodemax[j]++;  } 
     }  
     ij=1;  /*************** linmin ************************/
   /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
   resets p to where the function func(p) takes on a minimum along the direction xi from p ,
     for (i=1; i<=ncodemax[j]; i++) {  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
       for (k=0; k<=19; k++) {  the value of func at the returned location p . This is actually all accomplished by calling the
         if (Ndum[k] != 0) {  routines mnbrak and brent .*/
           nbcode[Tvar[j]][ij]=k;  int ncom; 
            double *pcom,*xicom;
           ij++;  double (*nrfunc)(double []); 
         }   
         if (ij > ncodemax[j]) break;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       }    { 
     }    double brent(double ax, double bx, double cx, 
   }                   double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
  for (k=0; k<19; k++) Ndum[k]=0;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
  for (i=1; i<=ncovmodel-2; i++) {    int j; 
       ij=Tvar[i];    double xx,xmin,bx,ax; 
       Ndum[ij]++;    double fx,fb,fa;
     }  
     double scale=10., axs, xxs, xxss; /* Scale added for infinity */
  ij=1;   
  for (i=1; i<=10; i++) {    ncom=n; 
    if((Ndum[i]!=0) && (i<=ncovcol)){    pcom=vector(1,n); 
      Tvaraff[ij]=i;    xicom=vector(1,n); 
      ij++;    nrfunc=func; 
    }    for (j=1;j<=n;j++) { 
  }      pcom[j]=p[j]; 
        xicom[j]=xi[j]; 
     cptcoveff=ij-1;    } 
 }  
     axs=0.0;
 /*********** Health Expectancies ****************/    xxss=1; /* 1 and using scale */
     xxs=1;
 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 )    do{
       ax=0.;
 {      xx= xxs;
   /* Health expectancies */      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
   double age, agelim, hf;      /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
   double ***p3mat,***varhe;      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
   double **dnewm,**doldm;      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
   double *xp;      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
   double **gp, **gm;      /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
   double ***gradg, ***trgradg;      if (fx != fx){
   int theta;          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
           printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);      }
   xp=vector(1,npar);    }while(fx != fx);
   dnewm=matrix(1,nlstate*2,1,npar);  
   doldm=matrix(1,nlstate*2,1,nlstate*2);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
      /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
   fprintf(ficreseij,"# Health expectancies\n");    /* fmin = f(p[j] + xmin * xi[j]) */
   fprintf(ficreseij,"# Age");    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
   for(i=1; i<=nlstate;i++)    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
     for(j=1; j<=nlstate;j++)  #ifdef DEBUG
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   fprintf(ficreseij,"\n");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
   if(estepm < stepm){    /* printf("linmin end "); */
     printf ("Problem %d lower than %d\n",estepm, stepm);    for (j=1;j<=n;j++) { 
   }      /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
   else  hstepm=estepm;        xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
   /* We compute the life expectancy from trapezoids spaced every estepm months      /* if(xxs <1.0) */
    * This is mainly to measure the difference between two models: for example      /*   printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */
    * if stepm=24 months pijx are given only every 2 years and by summing them      p[j] += xi[j]; /* Parameters values are updated accordingly */
    * we are calculating an estimate of the Life Expectancy assuming a linear    } 
    * progression inbetween and thus overestimating or underestimating according    /* printf("\n"); */
    * to the curvature of the survival function. If, for the same date, we    /* printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", *fret, (*func)(p)); */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    free_vector(xicom,1,n); 
    * to compare the new estimate of Life expectancy with the same linear    free_vector(pcom,1,n); 
    * hypothesis. A more precise result, taking into account a more precise  } 
    * curvature will be obtained if estepm is as small as stepm. */  
   
   /* For example we decided to compute the life expectancy with the smallest unit */  /*************** powell ************************/
   /* 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  Minimization of a function func of n variables. Input consists of an initial starting point
      nstepm is the number of stepm from age to agelin.  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
      Look at hpijx to understand the reason of that which relies in memory size  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
      and note for a fixed period like estepm months */  such that failure to decrease by more than this amount on one iteration signals doneness. On
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
      survival function given by stepm (the optimization length). Unfortunately it  function value at p , and iter is the number of iterations taken. The routine linmin is used.
      means that if the survival funtion is printed only each two years of age and if   */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
      results. So we changed our mind and took the option of the best precision.              double (*func)(double [])) 
   */  { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   agelim=AGESUP;    int i,ibig,j; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double del,t,*pt,*ptt,*xit;
     /* nhstepm age range expressed in number of stepm */    double directest;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    double fp,fptt;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    double *xits;
     /* if (stepm >= YEARM) hstepm=1;*/    int niterf, itmp;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    pt=vector(1,n); 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    ptt=vector(1,n); 
     gp=matrix(0,nhstepm,1,nlstate*2);    xit=vector(1,n); 
     gm=matrix(0,nhstepm,1,nlstate*2);    xits=vector(1,n); 
     *fret=(*func)(p); 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    for (j=1;j<=n;j++) pt[j]=p[j]; 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      rcurr_time = time(NULL);  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      for (*iter=1;;++(*iter)) { 
        fp=(*fret); /* From former iteration or initial value */
       ibig=0; 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      del=0.0; 
       rlast_time=rcurr_time;
     /* Computing Variances of health expectancies */      /* (void) gettimeofday(&curr_time,&tzp); */
       rcurr_time = time(NULL);  
      for(theta=1; theta <=npar; theta++){      curr_time = *localtime(&rcurr_time);
       for(i=1; i<=npar; i++){      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
       }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);       for (i=1;i<=n;i++) {
          printf(" %d %.12f",i, p[i]);
       cptj=0;        fprintf(ficlog," %d %.12lf",i, p[i]);
       for(j=1; j<= nlstate; j++){        fprintf(ficrespow," %.12lf", p[i]);
         for(i=1; i<=nlstate; i++){      }
           cptj=cptj+1;      printf("\n");
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      fprintf(ficlog,"\n");
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      fprintf(ficrespow,"\n");fflush(ficrespow);
           }      if(*iter <=3){
         }        tml = *localtime(&rcurr_time);
       }        strcpy(strcurr,asctime(&tml));
              rforecast_time=rcurr_time; 
              itmp = strlen(strcurr);
       for(i=1; i<=npar; i++)        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          strcurr[itmp-1]='\0';
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
              fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       cptj=0;        for(niterf=10;niterf<=30;niterf+=10){
       for(j=1; j<= nlstate; j++){          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         for(i=1;i<=nlstate;i++){          forecast_time = *localtime(&rforecast_time);
           cptj=cptj+1;          strcpy(strfor,asctime(&forecast_time));
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          itmp = strlen(strfor);
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          if(strfor[itmp-1]=='\n')
           }          strfor[itmp-1]='\0';
         }          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       for(j=1; j<= nlstate*2; j++)        }
         for(h=0; h<=nhstepm-1; h++){      }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      for (i=1;i<=n;i++) { /* For each direction i */
         }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
      }        fptt=(*fret); 
      #ifdef DEBUG
 /* End theta */            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
             fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  #endif
             printf("%d",i);fflush(stdout); /* print direction (parameter) i */
      for(h=0; h<=nhstepm-1; h++)        fprintf(ficlog,"%d",i);fflush(ficlog);
       for(j=1; j<=nlstate*2;j++)        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
         for(theta=1; theta <=npar; theta++)                                      /* Outputs are fret(new point p) p is updated and xit rescaled */
           trgradg[h][j][theta]=gradg[h][theta][j];        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
                /* because that direction will be replaced unless the gain del is small */
           /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
      for(i=1;i<=nlstate*2;i++)          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
       for(j=1;j<=nlstate*2;j++)          /* with the new direction. */
         varhe[i][j][(int)age] =0.;          del=fabs(fptt-(*fret)); 
           ibig=i; 
      printf("%d|",(int)age);fflush(stdout);        } 
      for(h=0;h<=nhstepm-1;h++){  #ifdef DEBUG
       for(k=0;k<=nhstepm-1;k++){        printf("%d %.12e",i,(*fret));
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        fprintf(ficlog,"%d %.12e",i,(*fret));
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        for (j=1;j<=n;j++) {
         for(i=1;i<=nlstate*2;i++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           for(j=1;j<=nlstate*2;j++)          printf(" x(%d)=%.12e",j,xit[j]);
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
     }        for(j=1;j<=n;j++) {
     /* Computing expectancies */          printf(" p(%d)=%.12e",j,p[j]);
     for(i=1; i<=nlstate;i++)          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       for(j=1; j<=nlstate;j++)        }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        printf("\n");
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        fprintf(ficlog,"\n");
            #endif
 /* 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]);*/      } /* end loop on each direction i */
       /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
         }      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
       /* New value of last point Pn is not computed, P(n-1) */
     fprintf(ficreseij,"%3.0f",age );      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
     cptj=0;        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
     for(i=1; i<=nlstate;i++)        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
       for(j=1; j<=nlstate;j++){        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
         cptj++;        /* decreased of more than 3.84  */
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
       }        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
     fprintf(ficreseij,"\n");        /* By adding 10 parameters more the gain should be 18.31 */
      
     free_matrix(gm,0,nhstepm,1,nlstate*2);        /* Starting the program with initial values given by a former maximization will simply change */
     free_matrix(gp,0,nhstepm,1,nlstate*2);        /* the scales of the directions and the directions, because the are reset to canonical directions */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #ifdef DEBUG
   }        int k[2],l;
   printf("\n");        k[0]=1;
         k[1]=-1;
   free_vector(xp,1,npar);        printf("Max: %.12e",(*func)(p));
   free_matrix(dnewm,1,nlstate*2,1,npar);        fprintf(ficlog,"Max: %.12e",(*func)(p));
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        for (j=1;j<=n;j++) {
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          printf(" %.12e",p[j]);
 }          fprintf(ficlog," %.12e",p[j]);
         }
 /************ Variance ******************/        printf("\n");
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)        fprintf(ficlog,"\n");
 {        for(l=0;l<=1;l++) {
   /* Variance of health expectancies */          for (j=1;j<=n;j++) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   double **newm;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double **dnewm,**doldm;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int i, j, nhstepm, hstepm, h, nstepm ;          }
   int k, cptcode;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double *xp;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double **gp, **gm;        }
   double ***gradg, ***trgradg;  #endif
   double ***p3mat;  
   double age,agelim, hf;  
   int theta;        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
   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");        free_vector(ptt,1,n); 
   fprintf(ficresvij,"# Age");        free_vector(pt,1,n); 
   for(i=1; i<=nlstate;i++)        return; 
     for(j=1; j<=nlstate;j++)      } 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   fprintf(ficresvij,"\n");      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
         ptt[j]=2.0*p[j]-pt[j]; 
   xp=vector(1,npar);        xit[j]=p[j]-pt[j]; 
   dnewm=matrix(1,nlstate,1,npar);        pt[j]=p[j]; 
   doldm=matrix(1,nlstate,1,nlstate);      } 
        fptt=(*func)(ptt); /* f_3 */
   if(estepm < stepm){      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
     printf ("Problem %d lower than %d\n",estepm, stepm);        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
   }        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
   else  hstepm=estepm;          /* Let f"(x2) be the 2nd derivative equal everywhere.  */
   /* For example we decided to compute the life expectancy with the smallest unit */        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
      nhstepm is the number of hstepm from age to agelim        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
      nstepm is the number of stepm from age to agelin.        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
      Look at hpijx to understand the reason of that which relies in memory size  #ifdef NRCORIGINAL
      and note for a fixed period like k years */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  #else
      survival function given by stepm (the optimization length). Unfortunately it        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
      means that if the survival funtion is printed only each two years of age and if        t= t- del*SQR(fp-fptt);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  #endif
      results. So we changed our mind and took the option of the best precision.        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
   */  #ifdef DEBUG
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        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);
   agelim = AGESUP;        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        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);
     gp=matrix(0,nhstepm,1,nlstate);        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);
     gm=matrix(0,nhstepm,1,nlstate);  #endif
   #ifdef POWELLORIGINAL
     for(theta=1; theta <=npar; theta++){        if (t < 0.0) { /* Then we use it for new direction */
       for(i=1; i<=npar; i++){ /* Computes gradient */  #else
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        if (directest*t < 0.0) { /* Contradiction between both tests */
       }        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        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);
       if (popbased==1) {      } 
         for(i=1; i<=nlstate;i++)        if (directest < 0.0) { /* Then we use it for new direction */
           prlim[i][i]=probs[(int)age][i][ij];  #endif
       }          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
            for (j=1;j<=n;j++) { 
       for(j=1; j<= nlstate; j++){            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
         for(h=0; h<=nhstepm; h++){            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          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);
       }  
      #ifdef DEBUG
       for(i=1; i<=npar; i++) /* Computes gradient */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(j=1;j<=n;j++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            printf(" %.12e",xit[j]);
              fprintf(ficlog," %.12e",xit[j]);
       if (popbased==1) {          }
         for(i=1; i<=nlstate;i++)          printf("\n");
           prlim[i][i]=probs[(int)age][i][ij];          fprintf(ficlog,"\n");
       }  #endif
         } /* end of t negative */
       for(j=1; j<= nlstate; j++){      } /* end if (fptt < fp)  */
         for(h=0; h<=nhstepm; h++){    } 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  } 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  /**** Prevalence limit (stable or period prevalence)  ****************/
       }  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       for(j=1; j<= nlstate; j++)  {
         for(h=0; h<=nhstepm; h++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];       matrix by transitions matrix until convergence is reached */
         }    
     } /* End theta */    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /* double **matprod2(); */ /* test */
     double **out, cov[NCOVMAX+1], **pmij();
     for(h=0; h<=nhstepm; h++)    double **newm;
       for(j=1; j<=nlstate;j++)    double agefin, delaymax=50 ; /* Max number of years to converge */
         for(theta=1; theta <=npar; theta++)    
           trgradg[h][j][theta]=gradg[h][theta][j];    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1;i<=nlstate;i++)      }
       for(j=1;j<=nlstate;j++)    
         vareij[i][j][(int)age] =0.;    cov[1]=1.;
     
     for(h=0;h<=nhstepm;h++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for(k=0;k<=nhstepm;k++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      newm=savm;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      /* Covariates have to be included here again */
         for(i=1;i<=nlstate;i++)      cov[2]=agefin;
           for(j=1;j<=nlstate;j++)      if(nagesqr==1)
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        cov[3]= agefin*agefin;;
       }      for (k=1; k<=cptcovn;k++) {
     }        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*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]]);*/
     fprintf(ficresvij,"%.0f ",age );      }
     for(i=1; i<=nlstate;i++)      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(j=1; j<=nlstate;j++){      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      for (k=1; k<=cptcovprod;k++) /* Useless */
       }        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     fprintf(ficresvij,"\n");      
     free_matrix(gp,0,nhstepm,1,nlstate);      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     free_matrix(gm,0,nhstepm,1,nlstate);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   } /* End age */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
        
   free_vector(xp,1,npar);      savm=oldm;
   free_matrix(doldm,1,nlstate,1,npar);      oldm=newm;
   free_matrix(dnewm,1,nlstate,1,nlstate);      maxmax=0.;
       for(j=1;j<=nlstate;j++){
 }        min=1.;
         max=0.;
 /************ Variance of prevlim ******************/        for(i=1; i<=nlstate; i++) {
 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)          sumnew=0;
 {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* Variance of prevalence limit */          prlim[i][j]= newm[i][j]/(1-sumnew);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
   double **newm;          max=FMAX(max,prlim[i][j]);
   double **dnewm,**doldm;          min=FMIN(min,prlim[i][j]);
   int i, j, nhstepm, hstepm;        }
   int k, cptcode;        maxmin=max-min;
   double *xp;        maxmax=FMAX(maxmax,maxmin);
   double *gp, *gm;      } /* j loop */
   double **gradg, **trgradg;      if(maxmax < ftolpl){
   double age,agelim;        return prlim;
   int theta;      }
        } /* age loop */
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    return prlim; /* should not reach here */
   fprintf(ficresvpl,"# Age");  }
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);  /*************** transition probabilities ***************/ 
   fprintf(ficresvpl,"\n");  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   xp=vector(1,npar);  {
   dnewm=matrix(1,nlstate,1,npar);    /* According to parameters values stored in x and the covariate's values stored in cov,
   doldm=matrix(1,nlstate,1,nlstate);       computes the probability to be observed in state j being in state i by appying the
         model to the ncovmodel covariates (including constant and age).
   hstepm=1*YEARM; /* Every year of age */       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   agelim = AGESUP;       ncth covariate in the global vector x is given by the formula:
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     if (stepm >= YEARM) hstepm=1;       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
     gradg=matrix(1,npar,1,nlstate);       Outputs ps[i][j] the probability to be observed in j being in j according to
     gp=vector(1,nlstate);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     gm=vector(1,nlstate);    */
     double s1, lnpijopii;
     for(theta=1; theta <=npar; theta++){    /*double t34;*/
       for(i=1; i<=npar; i++){ /* Computes gradient */    int i,j, nc, ii, jj;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }      for(i=1; i<= nlstate; i++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(j=1; j<i;j++){
       for(i=1;i<=nlstate;i++)          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         gp[i] = prlim[i][i];            /*lnpijopii += param[i][j][nc]*cov[nc];*/
                lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
       for(i=1; i<=npar; i++) /* Computes gradient */  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       for(i=1;i<=nlstate;i++)  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         gm[i] = prlim[i][i];        }
         for(j=i+1; j<=nlstate+ndeath;j++){
       for(i=1;i<=nlstate;i++)          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     } /* End theta */            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     trgradg =matrix(1,nlstate,1,npar);          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     for(j=1; j<=nlstate;j++)        }
       for(theta=1; theta <=npar; theta++)      }
         trgradg[j][theta]=gradg[theta][j];      
       for(i=1; i<= nlstate; i++){
     for(i=1;i<=nlstate;i++)        s1=0;
       varpl[i][(int)age] =0.;        for(j=1; j<i; j++){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     for(i=1;i<=nlstate;i++)        }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        for(j=i+1; j<=nlstate+ndeath; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     fprintf(ficresvpl,"%.0f ",age );          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     for(i=1; i<=nlstate;i++)        }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
     fprintf(ficresvpl,"\n");        ps[i][i]=1./(s1+1.);
     free_vector(gp,1,nlstate);        /* Computing other pijs */
     free_vector(gm,1,nlstate);        for(j=1; j<i; j++)
     free_matrix(gradg,1,npar,1,nlstate);          ps[i][j]= exp(ps[i][j])*ps[i][i];
     free_matrix(trgradg,1,nlstate,1,npar);        for(j=i+1; j<=nlstate+ndeath; j++)
   } /* End age */          ps[i][j]= exp(ps[i][j])*ps[i][i];
         /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   free_vector(xp,1,npar);      } /* end i */
   free_matrix(doldm,1,nlstate,1,npar);      
   free_matrix(dnewm,1,nlstate,1,nlstate);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(jj=1; jj<= nlstate+ndeath; jj++){
 }          ps[ii][jj]=0;
           ps[ii][ii]=1;
 /************ 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)      }
 {      
   int i, j,  i1, k1, l1;      
   int k2, l2, j1,  z1;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   int k=0,l, cptcode;      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   int first=1;      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;      /*   } */
   double **dnewm,**doldm;      /*   printf("\n "); */
   double *xp;      /* } */
   double *gp, *gm;      /* printf("\n ");printf("%lf ",cov[2]);*/
   double **gradg, **trgradg;      /*
   double **mu;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double age,agelim, cov[NCOVMAX];        goto end;*/
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */      return ps;
   int theta;  }
   char fileresprob[FILENAMELENGTH];  
   char fileresprobcov[FILENAMELENGTH];  /**************** Product of 2 matrices ******************/
   char fileresprobcor[FILENAMELENGTH];  
   double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   double ***varpij;  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   strcpy(fileresprob,"prob");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   strcat(fileresprob,fileres);    /* in, b, out are matrice of pointers which should have been initialized 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {       before: only the contents of out is modified. The function returns
     printf("Problem with resultfile: %s\n", fileresprob);       a pointer to pointers identical to out */
   }    int i, j, k;
   strcpy(fileresprobcov,"probcov");    for(i=nrl; i<= nrh; i++)
   strcat(fileresprobcov,fileres);      for(k=ncolol; k<=ncoloh; k++){
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {        out[i][k]=0.;
     printf("Problem with resultfile: %s\n", fileresprobcov);        for(j=ncl; j<=nch; j++)
   }          out[i][k] +=in[i][j]*b[j][k];
   strcpy(fileresprobcor,"probcor");      }
   strcat(fileresprobcor,fileres);    return out;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {  }
     printf("Problem with resultfile: %s\n", fileresprobcor);  
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  /************* Higher Matrix Product ***************/
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
    {
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    /* Computes the transition matrix starting at age 'age' over 
   fprintf(ficresprob,"# Age");       'nhstepm*hstepm*stepm' months (i.e. until
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   fprintf(ficresprobcov,"# Age");       nhstepm*hstepm matrices. 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   fprintf(ficresprobcov,"# Age");       (typically every 2 years instead of every month which is too big 
        for the memory).
        Model is determined by parameters x and covariates have to be 
   for(i=1; i<=nlstate;i++)       included manually here. 
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);       */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    int i, j, d, h, k;
     }      double **out, cov[NCOVMAX+1];
   fprintf(ficresprob,"\n");    double **newm;
   fprintf(ficresprobcov,"\n");    double agexact;
   fprintf(ficresprobcor,"\n");  
   xp=vector(1,npar);    /* Hstepm could be zero and should return the unit matrix */
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    for (i=1;i<=nlstate+ndeath;i++)
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));      for (j=1;j<=nlstate+ndeath;j++){
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   first=1;      }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    for(h=1; h <=nhstepm; h++){
     exit(0);      for(d=1; d <=hstepm; d++){
   }        newm=savm;
   else{        /* Covariates have to be included here again */
     fprintf(ficgp,"\n# Routine varprob");        cov[1]=1.;
   }        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        cov[2]=agexact;
     printf("Problem with html file: %s\n", optionfilehtm);        if(nagesqr==1)
     exit(0);          cov[3]= agexact*agexact;
   }        for (k=1; k<=cptcovn;k++) 
   else{          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
     fprintf(fichtm,"\n<br> We 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");          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     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");          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   }          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   cov[1]=1;  
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   j1=0;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   for(k1=1; k1<=1;k1++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     for(i1=1; i1<=ncodemax[k1];i1++){                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     j1++;        savm=oldm;
         oldm=newm;
     if  (cptcovn>0) {      }
       fprintf(ficresprob, "\n#********** Variable ");      for(i=1; i<=nlstate+ndeath; i++)
       fprintf(ficresprobcov, "\n#********** Variable ");        for(j=1;j<=nlstate+ndeath;j++) {
       fprintf(ficgp, "\n#********** Variable ");          po[i][j][h]=newm[i][j];
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       fprintf(ficresprobcor, "\n#********** Variable ");        }
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      /*printf("h=%d ",h);*/
       fprintf(ficresprob, "**********\n#");    } /* end h */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /*     printf("\n H=%d \n",h); */
       fprintf(ficresprobcov, "**********\n#");    return po;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  }
       fprintf(ficgp, "**********\n#");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  #ifdef NLOPT
       fprintf(ficgp, "**********\n#");    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double fret;
       fprintf(fichtm, "**********\n#");    double *xt;
     }    int j;
        myfunc_data *d2 = (myfunc_data *) pd;
       for (age=bage; age<=fage; age ++){  /* xt = (p1-1); */
         cov[2]=age;    xt=vector(1,n); 
         for (k=1; k<=cptcovn;k++) {    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  
         }    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
         for (k=1; k<=cptcovprod;k++)    printf("Function = %.12lf ",fret);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
            printf("\n");
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));   free_vector(xt,1,n);
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    return fret;
         gp=vector(1,(nlstate)*(nlstate+ndeath));  }
         gm=vector(1,(nlstate)*(nlstate+ndeath));  #endif
      
         for(theta=1; theta <=npar; theta++){  /*************** log-likelihood *************/
           for(i=1; i<=npar; i++)  double func( double *x)
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
              int i, ii, j, k, mi, d, kk;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
              double **out;
           k=0;    double sw; /* Sum of weights */
           for(i=1; i<= (nlstate); i++){    double lli; /* Individual log likelihood */
             for(j=1; j<=(nlstate+ndeath);j++){    int s1, s2;
               k=k+1;    double bbh, survp;
               gp[k]=pmmij[i][j];    long ipmx;
             }    double agexact;
           }    /*extern weight */
              /* We are differentiating ll according to initial status */
           for(i=1; i<=npar; i++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    /*for(i=1;i<imx;i++) 
          printf(" %d\n",s[4][i]);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    */
           k=0;  
           for(i=1; i<=(nlstate); i++){    ++countcallfunc;
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;    cov[1]=1.;
               gm[k]=pmmij[i][j];  
             }    for(k=1; k<=nlstate; k++) ll[k]=0.;
           }  
          if(mle==1){
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          /* Computes the values of the ncovmodel covariates of the model
         }           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
            Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)           to be observed in j being in i according to the model.
           for(theta=1; theta <=npar; theta++)         */
             trgradg[j][theta]=gradg[theta][j];        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
                    cov[2+nagesqr+k]=covar[Tvar[k]][i];
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);        }
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
                   is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
         pmij(pmmij,cov,ncovmodel,x,nlstate);           has been calculated etc */
                for(mi=1; mi<= wav[i]-1; mi++){
         k=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=1; i<=(nlstate); i++){            for (j=1;j<=nlstate+ndeath;j++){
           for(j=1; j<=(nlstate+ndeath);j++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             k=k+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             mu[k][(int) age]=pmmij[i][j];            }
           }          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)            cov[2]=agexact;
             varpij[i][j][(int)age] = doldm[i][j];            if(nagesqr==1)
               cov[3]= agexact*agexact;
         /*printf("\n%d ",(int)age);            for (kk=1; kk<=cptcovage;kk++) {
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            }
      }*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         fprintf(ficresprob,"\n%d ",(int)age);            savm=oldm;
         fprintf(ficresprobcov,"\n%d ",(int)age);            oldm=newm;
         fprintf(ficresprobcor,"\n%d ",(int)age);          } /* end mult */
         
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));          /* But now since version 0.9 we anticipate for bias at large stepm.
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);           * (in months) between two waves is not a multiple of stepm, we rounded to 
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);           * the nearest (and in case of equal distance, to the lowest) interval but now
         }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         i=0;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         for (k=1; k<=(nlstate);k++){           * probability in order to take into account the bias as a fraction of the way
           for (l=1; l<=(nlstate+ndeath);l++){           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
             i=i++;           * -stepm/2 to stepm/2 .
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);           * For stepm=1 the results are the same as for previous versions of Imach.
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);           * For stepm > 1 the results are less biased than in previous versions. 
             for (j=1; j<=i;j++){           */
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);          s1=s[mw[mi][i]][i];
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));          s2=s[mw[mi+1][i]][i];
             }          bbh=(double)bh[mi][i]/(double)stepm; 
           }          /* bias bh is positive if real duration
         }/* end of loop for state */           * is higher than the multiple of stepm and negative otherwise.
       } /* end of loop for age */           */
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       for (k1=1; k1<=(nlstate);k1++){          if( s2 > nlstate){ 
         for (l1=1; l1<=(nlstate+ndeath);l1++){            /* i.e. if s2 is a death state and if the date of death is known 
           if(l1==k1) continue;               then the contribution to the likelihood is the probability to 
           i=(k1-1)*(nlstate+ndeath)+l1;               die between last step unit time and current  step unit time, 
           for (k2=1; k2<=(nlstate);k2++){               which is also equal to probability to die before dh 
             for (l2=1; l2<=(nlstate+ndeath);l2++){               minus probability to die before dh-stepm . 
               if(l2==k2) continue;               In version up to 0.92 likelihood was computed
               j=(k2-1)*(nlstate+ndeath)+l2;          as if date of death was unknown. Death was treated as any other
               if(j<=i) continue;          health state: the date of the interview describes the actual state
               for (age=bage; age<=fage; age ++){          and not the date of a change in health state. The former idea was
                 if ((int)age %5==0){          to consider that at each interview the state was recorded
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;          (healthy, disable or death) and IMaCh was corrected; but when we
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;          introduced the exact date of death then we should have modified
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;          the contribution of an exact death to the likelihood. This new
                   mu1=mu[i][(int) age]/stepm*YEARM ;          contribution is smaller and very dependent of the step unit
                   mu2=mu[j][(int) age]/stepm*YEARM;          stepm. It is no more the probability to die between last interview
                   /* Computing eigen value of matrix of covariance */          and month of death but the probability to survive from last
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));          interview up to one month before death multiplied by the
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));          probability to die within a month. Thanks to Chris
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);          Jackson for correcting this bug.  Former versions increased
                   /* Eigen vectors */          mortality artificially. The bad side is that we add another loop
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));          which slows down the processing. The difference can be up to 10%
                   v21=sqrt(1.-v11*v11);          lower mortality.
                   v12=-v21;            */
                   v22=v11;          /* If, at the beginning of the maximization mostly, the
                   /*printf(fignu*/             cumulative probability or probability to be dead is
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */             constant (ie = 1) over time d, the difference is equal to
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */             0.  out[s1][3] = savm[s1][3]: probability, being at state
                   if(first==1){             s1 at precedent wave, to be dead a month before current
                     first=0;             wave is equal to probability, being at state s1 at
                     fprintf(ficgp,"\nset parametric;set nolabel");             precedent wave, to be dead at mont of the current
                     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);             wave. Then the observed probability (that this person died)
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");             is null according to current estimated parameter. In fact,
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);             it should be very low but not zero otherwise the log go to
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);             infinity.
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);          */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  /* #ifdef INFINITYORIGINAL */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
                     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\"",\  /* #else */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  /*          lli=log(mytinydouble); */
                   }else{  /*        else */
                     first=0;  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  /* #endif */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);              lli=log(out[s1][s2] - savm[s1][s2]);
                     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\"",\  
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \          } else if  (s2==-2) {
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);            for (j=1,survp=0. ; j<=nlstate; j++) 
                   }/* if first */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                 } /* age mod 5 */            /*survp += out[s1][j]; */
               } /* end loop age */            lli= log(survp);
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);          }
               first=1;          
             } /*l12 */          else if  (s2==-4) { 
           } /* k12 */            for (j=3,survp=0. ; j<=nlstate; j++)  
         } /*l1 */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }/* k1 */            lli= log(survp); 
     } /* loop covariates */          } 
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          else if  (s2==-5) { 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            for (j=1,survp=0. ; j<=2; j++)  
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            lli= log(survp); 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          } 
   }          
   free_vector(xp,1,npar);          else{
   fclose(ficresprob);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fclose(ficresprobcov);            /*  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 */
   fclose(ficresprobcor);          } 
   fclose(ficgp);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   fclose(fichtm);          /*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); */
           ipmx +=1;
           sw += weight[i];
 /******************* Printing html file ***********/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          /* if (lli < log(mytinydouble)){ */
                   int lastpass, int stepm, int weightopt, char model[],\          /*   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 imx,int jmin, int jmax, double jmeanint,char rfileres[],\          /*   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]); */
                   int popforecast, int estepm ,\          /* } */
                   double jprev1, double mprev1,double anprev1, \        } /* end of wave */
                   double jprev2, double mprev2,double anprev2){      } /* end of individual */
   int jj1, k1, i1, cpt;    }  else if(mle==2){
   /*char optionfilehtm[FILENAMELENGTH];*/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
     printf("Problem with %s \n",optionfilehtm), exit(0);        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  - 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              savm[ii][j]=(ii==j ? 1.0 : 0.0);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n            }
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n          for(d=0; d<=dh[mi][i]; d++){
  - Life expectancies by age and initial health status (estepm=%2d months):            newm=savm;
    <a href=\"e%s\">e%s</a> <br>\n</li>", \            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);            cov[2]=agexact;
             if(nagesqr==1)
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n              cov[3]= agexact*agexact;
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n            for (kk=1; kk<=cptcovage;kk++) {
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n            }
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n            savm=oldm;
  - 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);            oldm=newm;
           } /* end mult */
  if(popforecast==1) fprintf(fichtm,"\n        
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          s1=s[mw[mi][i]][i];
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          s2=s[mw[mi+1][i]][i];
         <br>",fileres,fileres,fileres,fileres);          bbh=(double)bh[mi][i]/(double)stepm; 
  else          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
    fprintf(fichtm,"\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);          ipmx +=1;
 fprintf(fichtm," <li>Graphs</li><p>");          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  m=cptcoveff;        } /* end of wave */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
  jj1=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  for(k1=1; k1<=m;k1++){        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
    for(i1=1; i1<=ncodemax[k1];i1++){        for(mi=1; mi<= wav[i]-1; mi++){
      jj1++;          for (ii=1;ii<=nlstate+ndeath;ii++)
      if (cptcovn > 0) {            for (j=1;j<=nlstate+ndeath;j++){
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        for (cpt=1; cpt<=cptcoveff;cpt++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          for(d=0; d<dh[mi][i]; d++){
      }            newm=savm;
      /* Pij */            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
      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>            cov[2]=agexact;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                if(nagesqr==1)
      /* Quasi-incidences */              cov[3]= agexact*agexact;
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>            for (kk=1; kk<=cptcovage;kk++) {
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
        /* Stable prevalence in each health state */            }
        for(cpt=1; cpt<nlstate;cpt++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            savm=oldm;
        }            oldm=newm;
     for(cpt=1; cpt<=nlstate;cpt++) {          } /* end mult */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        
 interval) in state (%d): v%s%d%d.png <br>          s1=s[mw[mi][i]][i];
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            s2=s[mw[mi+1][i]][i];
      }          bbh=(double)bh[mi][i]/(double)stepm; 
      for(cpt=1; cpt<=nlstate;cpt++) {          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(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>          ipmx +=1;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          sw += weight[i];
      }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        } /* end of wave */
 health expectancies in states (1) and (2): e%s%d.png<br>      } /* end of individual */
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
    }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  }        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
 fclose(fichtm);        for(mi=1; mi<= wav[i]-1; mi++){
 }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 /******************* Gnuplot file **************/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          for(d=0; d<dh[mi][i]; d++){
   int ng;            newm=savm;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
     printf("Problem with file %s",optionfilegnuplot);            cov[2]=agexact;
   }            if(nagesqr==1)
               cov[3]= agexact*agexact;
 #ifdef windows            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficgp,"cd \"%s\" \n",pathc);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
 #endif            }
 m=pow(2,cptcoveff);          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  /* 1eme*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (cpt=1; cpt<= nlstate ; cpt ++) {            savm=oldm;
    for (k1=1; k1<= m ; k1 ++) {            oldm=newm;
           } /* end mult */
 #ifdef windows        
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          s1=s[mw[mi][i]][i];
      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);          s2=s[mw[mi+1][i]][i];
 #endif          if( s2 > nlstate){ 
 #ifdef unix            lli=log(out[s1][s2] - savm[s1][s2]);
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          }else{
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 #endif          }
           ipmx +=1;
 for (i=1; i<= nlstate ; i ++) {          sw += weight[i];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  /*      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 */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      } /* end of individual */
     for (i=1; i<= nlstate ; i ++) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
 }        for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          for (ii=1;ii<=nlstate+ndeath;ii++)
      for (i=1; i<= nlstate ; i ++) {            for (j=1;j<=nlstate+ndeath;j++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }              }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          for(d=0; d<dh[mi][i]; d++){
 #ifdef unix            newm=savm;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
 #endif            cov[2]=agexact;
    }            if(nagesqr==1)
   }              cov[3]= agexact*agexact;
   /*2 eme*/            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
   for (k1=1; k1<= m ; k1 ++) {            }
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1; i<= nlstate+1 ; i ++) {            savm=oldm;
       k=2*i;            oldm=newm;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          } /* end mult */
       for (j=1; j<= nlstate+1 ; j ++) {        
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          s1=s[mw[mi][i]][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          s2=s[mw[mi+1][i]][i];
 }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          ipmx +=1;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          sw += weight[i];
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for (j=1; j<= nlstate+1 ; j ++) {          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        } /* end of wave */
         else fprintf(ficgp," \%%*lf (\%%*lf)");      } /* end of individual */
 }      } /* End of if */
       fprintf(ficgp,"\" t\"\" w l 0,");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for (j=1; j<= nlstate+1 ; j ++) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    return -l;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  /*************** log-likelihood *************/
       else fprintf(ficgp,"\" t\"\" w l 0,");  double funcone( double *x)
     }  {
   }    /* Same as likeli but slower because of a lot of printf and if */
      int i, ii, j, k, mi, d, kk;
   /*3eme*/    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
   for (k1=1; k1<= m ; k1 ++) {    double lli; /* Individual log likelihood */
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double llt;
       k=2+nlstate*(2*cpt-2);    int s1, s2;
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    double bbh, survp;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    double agexact;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    /*extern weight */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    /* We are differentiating ll according to initial status */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    /*for(i=1;i<imx;i++) 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      printf(" %d\n",s[4][i]);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    */
     cov[1]=1.;
 */  
       for (i=1; i< nlstate ; i ++) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);  
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
     }      for(mi=1; mi<= wav[i]-1; mi++){
   }        for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
   /* CV preval stat */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (k1=1; k1<= m ; k1 ++) {            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (cpt=1; cpt<nlstate ; cpt ++) {          }
       k=3;        for(d=0; d<dh[mi][i]; d++){
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          newm=savm;
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;
       for (i=1; i< nlstate ; i ++)          if(nagesqr==1)
         fprintf(ficgp,"+$%d",k+i+1);            cov[3]= agexact*agexact;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          for (kk=1; kk<=cptcovage;kk++) {
                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
       l=3+(nlstate+ndeath)*cpt;          }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         l=3+(nlstate+ndeath)*cpt;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         fprintf(ficgp,"+$%d",l+i+1);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
     }          savm=oldm;
   }            oldm=newm;
          } /* end mult */
   /* proba elementaires */        
    for(i=1,jk=1; i <=nlstate; i++){        s1=s[mw[mi][i]][i];
     for(k=1; k <=(nlstate+ndeath); k++){        s2=s[mw[mi+1][i]][i];
       if (k != i) {        bbh=(double)bh[mi][i]/(double)stepm; 
         for(j=1; j <=ncovmodel; j++){        /* bias is positive if real duration
                 * is higher than the multiple of stepm and negative otherwise.
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);         */
           jk++;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           fprintf(ficgp,"\n");          lli=log(out[s1][s2] - savm[s1][s2]);
         }        } else if  (s2==-2) {
       }          for (j=1,survp=0. ; j<=nlstate; j++) 
     }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
    }          lli= log(survp);
         }else if (mle==1){
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      for(jk=1; jk <=m; jk++) {        } else if(mle==2){
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          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 */
        if (ng==2)        } else if(mle==3){  /* exponential inter-extrapolation */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
        else        } else if (mle==4){  /* mle=4 no inter-extrapolation */
          fprintf(ficgp,"\nset title \"Probability\"\n");          lli=log(out[s1][s2]); /* Original formula */
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        } else{  /* mle=0 back to 1 */
        i=1;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        for(k2=1; k2<=nlstate; k2++) {          /*lli=log(out[s1][s2]); */ /* Original formula */
          k3=i;        } /* End of if */
          for(k=1; k<=(nlstate+ndeath); k++) {        ipmx +=1;
            if (k != k2){        sw += weight[i];
              if(ng==2)        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
              else        if(globpr){
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
              ij=1;   %11.6f %11.6f %11.6f ", \
              for(j=3; j <=ncovmodel; j++) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                  ij++;            llt +=ll[k]*gipmx/gsw;
                }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
                else          }
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          fprintf(ficresilk," %10.6f\n", -llt);
              }        }
              fprintf(ficgp,")/(1");      } /* end of wave */
                  } /* end of individual */
              for(k1=1; k1 <=nlstate; k1++){      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                ij=1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                for(j=3; j <=ncovmodel; j++){    if(globpr==0){ /* First time we count the contributions and weights */
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      gipmx=ipmx;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      gsw=sw;
                    ij++;    }
                  }    return -l;
                  else  }
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
                }  
                fprintf(ficgp,")");  /*************** function likelione ***********/
              }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);  {
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    /* This routine should help understanding what is done with 
              i=i+ncovmodel;       the selection of individuals/waves and
            }       to check the exact contribution to the likelihood.
          }       Plotting could be done.
        }     */
      }    int k;
    }  
    fclose(ficgp);    if(*globpri !=0){ /* Just counts and sums, no printings */
 }  /* end gnuplot */      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 /*************** Moving average **************/        printf("Problem with resultfile: %s\n", fileresilk);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
   int i, cpt, cptcod;      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       for (i=1; i<=nlstate;i++)      /*  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 (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      for(k=1; k<=nlstate; k++) 
           mobaverage[(int)agedeb][i][cptcod]=0.;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
          fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    }
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    *fretone=(*funcone)(p);
           for (cpt=0;cpt<=4;cpt++){    if(*globpri !=0){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      fclose(ficresilk);
           }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      fflush(fichtm); 
         }    } 
       }    return;
     }  }
      
 }  
   /*********** Maximum Likelihood Estimation ***************/
   
 /************** Forecasting ******************/  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){  {
      int i,j, iter=0;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    double **xi;
   int *popage;    double fret;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double fretone; /* Only one call to likelihood */
   double *popeffectif,*popcount;    /*  char filerespow[FILENAMELENGTH];*/
   double ***p3mat;  
   char fileresf[FILENAMELENGTH];  #ifdef NLOPT
     int creturn;
  agelim=AGESUP;    nlopt_opt opt;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     double *lb;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double minf; /* the minimum objective value, upon return */
      double * p1; /* Shifted parameters from 0 instead of 1 */
      myfunc_data dinst, *d = &dinst;
   strcpy(fileresf,"f");  #endif
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);    xi=matrix(1,npar,1,npar);
   }    for (i=1;i<=npar;i++)
   printf("Computing forecasting: result on file '%s' \n", fileresf);      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
   if (mobilav==1) {    strcat(filerespow,fileres);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     movingaverage(agedeb, fage, ageminpar, mobaverage);      printf("Problem with resultfile: %s\n", filerespow);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   if (stepm<=12) stepsize=1;    for (i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate+ndeath;j++)
   agelim=AGESUP;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
   hstepm=1;  #ifdef POWELL
   hstepm=hstepm/stepm;    powell(p,xi,npar,ftol,&iter,&fret,func);
   yp1=modf(dateintmean,&yp);  #endif
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);  #ifdef NLOPT
   mprojmean=yp;  #ifdef NEWUOA
   yp1=modf((yp2*30.5),&yp);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   jprojmean=yp;  #else
   if(jprojmean==0) jprojmean=1;    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   if(mprojmean==0) jprojmean=1;  #endif
      lb=vector(0,npar-1);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
      nlopt_set_lower_bounds(opt, lb);
   for(cptcov=1;cptcov<=i2;cptcov++){    nlopt_set_initial_step1(opt, 0.1);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
       k=k+1;    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
       fprintf(ficresf,"\n#******");    d->function = func;
       for(j=1;j<=cptcoveff;j++) {    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    nlopt_set_min_objective(opt, myfunc, d);
       }    nlopt_set_xtol_rel(opt, ftol);
       fprintf(ficresf,"******\n");    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       fprintf(ficresf,"# StartingAge FinalAge");      printf("nlopt failed! %d\n",creturn); 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    }
          else {
            printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
         fprintf(ficresf,"\n");      iter=1; /* not equal */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      }
     nlopt_destroy(opt);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  #endif
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_matrix(xi,1,npar,1,npar);
           nhstepm = nhstepm/hstepm;    fclose(ficrespow);
              printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
           oldm=oldms;savm=savms;    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
          }
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  /**** Computes Hessian and covariance matrix ***/
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
             }  {
             for(j=1; j<=nlstate+ndeath;j++) {    double  **a,**y,*x,pd;
               kk1=0.;kk2=0;    double **hess;
               for(i=1; i<=nlstate;i++) {                  int i, j;
                 if (mobilav==1)    int *indx;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
                 }    void lubksb(double **a, int npar, int *indx, double b[]) ;
                    void ludcmp(double **a, int npar, int *indx, double *d) ;
               }    double gompertz(double p[]);
               if (h==(int)(calagedate+12*cpt)){    hess=matrix(1,npar,1,npar);
                 fprintf(ficresf," %.3f", kk1);  
                            printf("\nCalculation of the hessian matrix. Wait...\n");
               }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
             }    for (i=1;i<=npar;i++){
           }      printf("%d",i);fflush(stdout);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"%d",i);fflush(ficlog);
         }     
       }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     }      
   }      /*  printf(" %f ",p[i]);
                  printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
     
   fclose(ficresf);    for (i=1;i<=npar;i++) {
 }      for (j=1;j<=npar;j++)  {
 /************** Forecasting ******************/        if (j>i) { 
 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){          printf(".%d%d",i,j);fflush(stdout);
            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   int *popage;          
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          hess[j][i]=hess[i][j];    
   double *popeffectif,*popcount;          /*printf(" %lf ",hess[i][j]);*/
   double ***p3mat,***tabpop,***tabpopprev;        }
   char filerespop[FILENAMELENGTH];      }
     }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("\n");
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficlog,"\n");
   agelim=AGESUP;  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    
      a=matrix(1,npar,1,npar);
      y=matrix(1,npar,1,npar);
   strcpy(filerespop,"pop");    x=vector(1,npar);
   strcat(filerespop,fileres);    indx=ivector(1,npar);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    for (i=1;i<=npar;i++)
     printf("Problem with forecast resultfile: %s\n", filerespop);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   }    ludcmp(a,npar,indx,&pd);
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
     for (j=1;j<=npar;j++) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   if (mobilav==1) {      lubksb(a,npar,indx,x);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1;i<=npar;i++){ 
     movingaverage(agedeb, fage, ageminpar, mobaverage);        matcov[i][j]=x[i];
   }      }
     }
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    printf("\n#Hessian matrix#\n");
      fprintf(ficlog,"\n#Hessian matrix#\n");
   agelim=AGESUP;    for (i=1;i<=npar;i++) { 
        for (j=1;j<=npar;j++) { 
   hstepm=1;        printf("%.3e ",hess[i][j]);
   hstepm=hstepm/stepm;        fprintf(ficlog,"%.3e ",hess[i][j]);
        }
   if (popforecast==1) {      printf("\n");
     if((ficpop=fopen(popfile,"r"))==NULL) {      fprintf(ficlog,"\n");
       printf("Problem with population file : %s\n",popfile);exit(0);    }
     }  
     popage=ivector(0,AGESUP);    /* Recompute Inverse */
     popeffectif=vector(0,AGESUP);    for (i=1;i<=npar;i++)
     popcount=vector(0,AGESUP);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
        ludcmp(a,npar,indx,&pd);
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    /*  printf("\n#Hessian matrix recomputed#\n");
      
     imx=i;    for (j=1;j<=npar;j++) {
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      for (i=1;i<=npar;i++) x[i]=0;
   }      x[j]=1;
       lubksb(a,npar,indx,x);
   for(cptcov=1;cptcov<=i2;cptcov++){      for (i=1;i<=npar;i++){ 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        y[i][j]=x[i];
       k=k+1;        printf("%.3e ",y[i][j]);
       fprintf(ficrespop,"\n#******");        fprintf(ficlog,"%.3e ",y[i][j]);
       for(j=1;j<=cptcoveff;j++) {      }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("\n");
       }      fprintf(ficlog,"\n");
       fprintf(ficrespop,"******\n");    }
       fprintf(ficrespop,"# Age");    */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");    free_matrix(a,1,npar,1,npar);
          free_matrix(y,1,npar,1,npar);
       for (cpt=0; cpt<=0;cpt++) {    free_vector(x,1,npar);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      free_ivector(indx,1,npar);
            free_matrix(hess,1,npar,1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  }
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*************** hessian matrix ****************/
           oldm=oldms;savm=savms;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    {
            int i;
           for (h=0; h<=nhstepm; h++){    int l=1, lmax=20;
             if (h==(int) (calagedate+YEARM*cpt)) {    double k1,k2;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    double p2[MAXPARM+1]; /* identical to x */
             }    double res;
             for(j=1; j<=nlstate+ndeath;j++) {    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
               kk1=0.;kk2=0;    double fx;
               for(i=1; i<=nlstate;i++) {                  int k=0,kmax=10;
                 if (mobilav==1)    double l1;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    fx=func(x);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    for (i=1;i<=npar;i++) p2[i]=x[i];
                 }    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
               }      l1=pow(10,l);
               if (h==(int)(calagedate+12*cpt)){      delts=delt;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      for(k=1 ; k <kmax; k=k+1){
                   /*fprintf(ficrespop," %.3f", kk1);        delt = delta*(l1*k);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        p2[theta]=x[theta] +delt;
               }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
             }        p2[theta]=x[theta]-delt;
             for(i=1; i<=nlstate;i++){        k2=func(p2)-fx;
               kk1=0.;        /*res= (k1-2.0*fx+k2)/delt/delt; */
                 for(j=1; j<=nlstate;j++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        
                 }  #ifdef DEBUGHESS
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-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);
             }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           }          k=kmax;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       }          k=kmax; l=lmax*10;
          }
   /******/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
       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)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    delti[theta]=delts;
           nhstepm = nhstepm/hstepm;    return res; 
              
           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);    double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
           for (h=0; h<=nhstepm; h++){  {
             if (h==(int) (calagedate+YEARM*cpt)) {    int i;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    int l=1, lmax=20;
             }    double k1,k2,k3,k4,res,fx;
             for(j=1; j<=nlstate+ndeath;j++) {    double p2[MAXPARM+1];
               kk1=0.;kk2=0;    int k;
               for(i=1; i<=nlstate;i++) {                
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        fx=func(x);
               }    for (k=1; k<=2; k++) {
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      for (i=1;i<=npar;i++) p2[i]=x[i];
             }      p2[thetai]=x[thetai]+delti[thetai]/k;
           }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      k1=func(p2)-fx;
         }    
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
    }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }      k2=func(p2)-fx;
      
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   if (popforecast==1) {      k3=func(p2)-fx;
     free_ivector(popage,0,AGESUP);    
     free_vector(popeffectif,0,AGESUP);      p2[thetai]=x[thetai]-delti[thetai]/k;
     free_vector(popcount,0,AGESUP);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }      k4=func(p2)-fx;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  #ifdef DEBUG
   fclose(ficrespop);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
 }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
 /***********************************************/    }
 /**************** Main Program *****************/    return res;
 /***********************************************/  }
   
 int main(int argc, char *argv[])  /************** Inverse of matrix **************/
 {  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int i,imax,j,k; 
   double agedeb, agefin,hf;    double big,dum,sum,temp; 
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double *vv; 
    
   double fret;    vv=vector(1,n); 
   double **xi,tmp,delta;    *d=1.0; 
     for (i=1;i<=n;i++) { 
   double dum; /* Dummy variable */      big=0.0; 
   double ***p3mat;      for (j=1;j<=n;j++) 
   int *indx;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   char line[MAXLINE], linepar[MAXLINE];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      vv[i]=1.0/big; 
   int firstobs=1, lastobs=10;    } 
   int sdeb, sfin; /* Status at beginning and end */    for (j=1;j<=n;j++) { 
   int c,  h , cpt,l;      for (i=1;i<j;i++) { 
   int ju,jl, mi;        sum=a[i][j]; 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        a[i][j]=sum; 
   int mobilav=0,popforecast=0;      } 
   int hstepm, nhstepm;      big=0.0; 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
   double bage, fage, age, agelim, agebase;        for (k=1;k<j;k++) 
   double ftolpl=FTOL;          sum -= a[i][k]*a[k][j]; 
   double **prlim;        a[i][j]=sum; 
   double *severity;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   double ***param; /* Matrix of parameters */          big=dum; 
   double  *p;          imax=i; 
   double **matcov; /* Matrix of covariance */        } 
   double ***delti3; /* Scale */      } 
   double *delti; /* Scale */      if (j != imax) { 
   double ***eij, ***vareij;        for (k=1;k<=n;k++) { 
   double **varpl; /* Variances of prevalence limits by age */          dum=a[imax][k]; 
   double *epj, vepp;          a[imax][k]=a[j][k]; 
   double kk1, kk2;          a[j][k]=dum; 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        } 
          *d = -(*d); 
         vv[imax]=vv[j]; 
   char *alph[]={"a","a","b","c","d","e"}, str[4];      } 
       indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
   char z[1]="c", occ;      if (j != n) { 
 #include <sys/time.h>        dum=1.0/(a[j][j]); 
 #include <time.h>        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      } 
      } 
   /* long total_usecs;    free_vector(vv,1,n);  /* Doesn't work */
   struct timeval start_time, end_time;  ;
    } 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   getcwd(pathcd, size);  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
   printf("\n%s",version);    int i,ii=0,ip,j; 
   if(argc <=1){    double sum; 
     printf("\nEnter the parameter file name: ");   
     scanf("%s",pathtot);    for (i=1;i<=n;i++) { 
   }      ip=indx[i]; 
   else{      sum=b[ip]; 
     strcpy(pathtot,argv[1]);      b[ip]=b[i]; 
   }      if (ii) 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   /*cygwin_split_path(pathtot,path,optionfile);      else if (sum) ii=i; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      b[i]=sum; 
   /* cutv(path,optionfile,pathtot,'\\');*/    } 
     for (i=n;i>=1;i--) { 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      sum=b[i]; 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   chdir(path);      b[i]=sum/a[i][i]; 
   replace(pathc,path);    } 
   } 
 /*-------- arguments in the command line --------*/  
   void pstamp(FILE *fichier)
   strcpy(fileres,"r");  {
   strcat(fileres, optionfilefiname);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   strcat(fileres,".txt");    /* Other files have txt extension */  }
   
   /*---------arguments file --------*/  /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  {  /* Some frequencies */
     printf("Problem with optionfile %s\n",optionfile);    
     goto end;    int i, m, jk, j1, bool, z1,j;
   }    int first;
     double ***freq; /* Frequencies */
   strcpy(filereso,"o");    double *pp, **prop;
   strcat(filereso,fileres);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   if((ficparo=fopen(filereso,"w"))==NULL) {    char fileresp[FILENAMELENGTH];
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    
   }    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
   /* Reads comments: lines beginning with '#' */    strcpy(fileresp,"p");
   while((c=getc(ficpar))=='#' && c!= EOF){    strcat(fileresp,fileres);
     ungetc(c,ficpar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     fgets(line, MAXLINE, ficpar);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     puts(line);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     fputs(line,ficparo);      exit(0);
   }    }
   ungetc(c,ficpar);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\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);    j=cptcoveff;
   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);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    first=1;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
     fputs(line,ficparo);    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   }    /*    j1++; */
   ungetc(c,ficpar);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
              scanf("%d", i);*/
   covar=matrix(0,NCOVMAX,1,n);        for (i=-5; i<=nlstate+ndeath; i++)  
   cptcovn=0;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
   ncovmodel=2+cptcovn;        
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        for (i=1; i<=nlstate; i++)  
            for(m=iagemin; m <= iagemax+3; m++)
   /* Read guess parameters */            prop[i][m]=0;
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        dateintsum=0;
     ungetc(c,ficpar);        k2cpt=0;
     fgets(line, MAXLINE, ficpar);        for (i=1; i<=imx; i++) {
     puts(line);          bool=1;
     fputs(line,ficparo);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
   }            for (z1=1; z1<=cptcoveff; z1++)       
   ungetc(c,ficpar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                    /* Tests if the value of each of the covariates of i is equal to filter j1 */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                bool=0;
     for(i=1; i <=nlstate; i++)                /* 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", 
     for(j=1; j <=nlstate+ndeath-1; j++){                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
       fscanf(ficpar,"%1d%1d",&i1,&j1);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
       fprintf(ficparo,"%1d%1d",i1,j1);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
       printf("%1d%1d",i,j);              } 
       for(k=1; k<=ncovmodel;k++){          }
         fscanf(ficpar," %lf",&param[i][j][k]);   
         printf(" %lf",param[i][j][k]);          if (bool==1){
         fprintf(ficparo," %lf",param[i][j][k]);            for(m=firstpass; m<=lastpass; m++){
       }              k2=anint[m][i]+(mint[m][i]/12.);
       fscanf(ficpar,"\n");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       printf("\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       fprintf(ficparo,"\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                  if (m<lastpass) {
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   p=param[1][1];                }
                  
   /* Reads comments: lines beginning with '#' */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   while((c=getc(ficpar))=='#' && c!= EOF){                  dateintsum=dateintsum+k2;
     ungetc(c,ficpar);                  k2cpt++;
     fgets(line, MAXLINE, ficpar);                }
     puts(line);                /*}*/
     fputs(line,ficparo);            }
   }          }
   ungetc(c,ficpar);        } /* end i */
          
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        pstamp(ficresp);
   for(i=1; i <=nlstate; i++){        if  (cptcovn>0) {
     for(j=1; j <=nlstate+ndeath-1; j++){          fprintf(ficresp, "\n#********** Variable "); 
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("%1d%1d",i,j);          fprintf(ficresp, "**********\n#");
       fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficlog, "\n#********** Variable "); 
       for(k=1; k<=ncovmodel;k++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fscanf(ficpar,"%le",&delti3[i][j][k]);          fprintf(ficlog, "**********\n#");
         printf(" %le",delti3[i][j][k]);        }
         fprintf(ficparo," %le",delti3[i][j][k]);        for(i=1; i<=nlstate;i++) 
       }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       fscanf(ficpar,"\n");        fprintf(ficresp, "\n");
       printf("\n");        
       fprintf(ficparo,"\n");        for(i=iagemin; i <= iagemax+3; i++){
     }          if(i==iagemax+3){
   }            fprintf(ficlog,"Total");
   delti=delti3[1][1];          }else{
              if(first==1){
   /* Reads comments: lines beginning with '#' */              first=0;
   while((c=getc(ficpar))=='#' && c!= EOF){              printf("See log file for details...\n");
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);            fprintf(ficlog,"Age %d", i);
     puts(line);          }
     fputs(line,ficparo);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   ungetc(c,ficpar);              pp[jk] += freq[jk][m][i]; 
            }
   matcov=matrix(1,npar,1,npar);          for(jk=1; jk <=nlstate ; jk++){
   for(i=1; i <=npar; i++){            for(m=-1, pos=0; m <=0 ; m++)
     fscanf(ficpar,"%s",&str);              pos += freq[jk][m][i];
     printf("%s",str);            if(pp[jk]>=1.e-10){
     fprintf(ficparo,"%s",str);              if(first==1){
     for(j=1; j <=i; j++){                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fscanf(ficpar," %le",&matcov[i][j]);              }
       printf(" %.5le",matcov[i][j]);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fprintf(ficparo," %.5le",matcov[i][j]);            }else{
     }              if(first==1)
     fscanf(ficpar,"\n");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     printf("\n");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     fprintf(ficparo,"\n");            }
   }          }
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)          for(jk=1; jk <=nlstate ; jk++){
       matcov[i][j]=matcov[j][i];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                  pp[jk] += freq[jk][m][i];
   printf("\n");          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
     /*-------- Rewriting paramater file ----------*/            posprop += prop[jk][i];
      strcpy(rfileres,"r");    /* "Rparameterfile */          }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          for(jk=1; jk <=nlstate ; jk++){
      strcat(rfileres,".");    /* */            if(pos>=1.e-5){
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              if(first==1)
     if((ficres =fopen(rfileres,"w"))==NULL) {                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     }            }else{
     fprintf(ficres,"#%s\n",version);              if(first==1)
                    printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     /*-------- data file ----------*/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     if((fic=fopen(datafile,"r"))==NULL)    {            }
       printf("Problem with datafile: %s\n", datafile);goto end;            if( i <= iagemax){
     }              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     n= lastobs;                /*probs[i][jk][j1]= pp[jk]/pos;*/
     severity = vector(1,maxwav);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     outcome=imatrix(1,maxwav+1,1,n);              }
     num=ivector(1,n);              else
     moisnais=vector(1,n);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     annais=vector(1,n);            }
     moisdc=vector(1,n);          }
     andc=vector(1,n);          
     agedc=vector(1,n);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     cod=ivector(1,n);            for(m=-1; m <=nlstate+ndeath; m++)
     weight=vector(1,n);              if(freq[jk][m][i] !=0 ) {
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              if(first==1)
     mint=matrix(1,maxwav,1,n);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     anint=matrix(1,maxwav,1,n);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     s=imatrix(1,maxwav+1,1,n);              }
     adl=imatrix(1,maxwav+1,1,n);              if(i <= iagemax)
     tab=ivector(1,NCOVMAX);            fprintf(ficresp,"\n");
     ncodemax=ivector(1,8);          if(first==1)
             printf("Others in log...\n");
     i=1;          fprintf(ficlog,"\n");
     while (fgets(line, MAXLINE, fic) != NULL)    {        }
       if ((i >= firstobs) && (i <=lastobs)) {        /*}*/
            }
         for (j=maxwav;j>=1;j--){    dateintmean=dateintsum/k2cpt; 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);   
           strcpy(line,stra);    fclose(ficresp);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(pp,1,nlstate);
         }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
            /* End of Freq */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
   /************ Prevalence ********************/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  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)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);       in each health status at the date of interview (if between dateprev1 and dateprev2).
         for (j=ncovcol;j>=1;j--){       We still use firstpass and lastpass as another selection.
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    */
         }   
         num[i]=atol(stra);    int i, m, jk, j1, bool, z1,j;
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    double **prop;
           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;}*/    double posprop; 
     double  y2; /* in fractional years */
         i=i+1;    int iagemin, iagemax;
       }    int first; /** to stop verbosity which is redirected to log file */
     }  
     /* printf("ii=%d", ij);    iagemin= (int) agemin;
        scanf("%d",i);*/    iagemax= (int) agemax;
   imx=i-1; /* Number of individuals */    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
   /* for (i=1; i<=imx; i++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    j1=0;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    /*j=cptcoveff;*/
     }*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    /*  for (i=1; i<=imx; i++){    
      if (s[4][i]==9)  s[4][i]=-1;    first=1;
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
        /*for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;*/
   /* Calculation of the number of parameter from char model*/        
   Tvar=ivector(1,15);        for (i=1; i<=nlstate; i++)  
   Tprod=ivector(1,15);          for(m=iagemin; m <= iagemax+3; m++)
   Tvaraff=ivector(1,15);            prop[i][m]=0.0;
   Tvard=imatrix(1,15,1,2);       
   Tage=ivector(1,15);              for (i=1; i<=imx; i++) { /* Each individual */
              bool=1;
   if (strlen(model) >1){          if  (cptcovn>0) {
     j=0, j1=0, k1=1, k2=1;            for (z1=1; z1<=cptcoveff; z1++) 
     j=nbocc(model,'+');              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     j1=nbocc(model,'*');                bool=0;
     cptcovn=j+1;          } 
     cptcovprod=j1;          if (bool==1) { 
                for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     strcpy(modelsav,model);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       printf("Error. Non available option model=%s ",model);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       goto end;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                    if (s[m][i]>0 && s[m][i]<=nlstate) { 
     for(i=(j+1); i>=1;i--){                  /*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]]);*/
       cutv(stra,strb,modelsav,'+');                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                  prop[s[m][i]][iagemax+3] += weight[i]; 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                } 
       /*scanf("%d",i);*/              }
       if (strchr(strb,'*')) {            } /* end selection of waves */
         cutv(strd,strc,strb,'*');          }
         if (strcmp(strc,"age")==0) {        }
           cptcovprod--;        for(i=iagemin; i <= iagemax+3; i++){  
           cutv(strb,stre,strd,'V');          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           Tvar[i]=atoi(stre);            posprop += prop[jk][i]; 
           cptcovage++;          } 
             Tage[cptcovage]=i;          
             /*printf("stre=%s ", stre);*/          for(jk=1; jk <=nlstate ; jk++){     
         }            if( i <=  iagemax){ 
         else if (strcmp(strd,"age")==0) {              if(posprop>=1.e-5){ 
           cptcovprod--;                probs[i][jk][j1]= prop[jk][i]/posprop;
           cutv(strb,stre,strc,'V');              } else{
           Tvar[i]=atoi(stre);                if(first==1){
           cptcovage++;                  first=0;
           Tage[cptcovage]=i;                  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]);
         }                }
         else {              }
           cutv(strb,stre,strc,'V');            } 
           Tvar[i]=ncovcol+k1;          }/* end jk */ 
           cutv(strb,strc,strd,'V');        }/* end i */ 
           Tprod[k1]=i;      /*} *//* end i1 */
           Tvard[k1][1]=atoi(strc);    } /* end j1 */
           Tvard[k1][2]=atoi(stre);    
           Tvar[cptcovn+k2]=Tvard[k1][1];    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    /*free_vector(pp,1,nlstate);*/
           for (k=1; k<=lastobs;k++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  }  /* End of prevalence */
           k1++;  
           k2=k2+2;  /************* Waves Concatenation ***************/
         }  
       }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       else {  {
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        /*  scanf("%d",i);*/       Death is a valid wave (if date is known).
       cutv(strd,strc,strb,'V');       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       Tvar[i]=atoi(strc);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       }       and mw[mi+1][i]. dh depends on stepm.
       strcpy(modelsav,stra);         */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/    int i, mi, m;
     }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 }       double sum=0., jmean=0.;*/
      int first;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    int j, k=0,jk, ju, jl;
   printf("cptcovprod=%d ", cptcovprod);    double sum=0.;
   scanf("%d ",i);*/    first=0;
     fclose(fic);    jmin=100000;
     jmax=-1;
     /*  if(mle==1){*/    jmean=0.;
     if (weightopt != 1) { /* Maximisation without weights*/    for(i=1; i<=imx; i++){
       for(i=1;i<=n;i++) weight[i]=1.0;      mi=0;
     }      m=firstpass;
     /*-calculation of age at interview from date of interview and age at death -*/      while(s[m][i] <= nlstate){
     agev=matrix(1,maxwav,1,imx);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           mw[++mi][i]=m;
     for (i=1; i<=imx; i++) {        if(m >=lastpass)
       for(m=2; (m<= maxwav); m++) {          break;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        else
          anint[m][i]=9999;          m++;
          s[m][i]=-1;      }/* end while */
        }      if (s[m][i] > nlstate){
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        mi++;     /* Death is another wave */
       }        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
         mw[mi][i]=m;
     for (i=1; i<=imx; i++)  {      }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){      wav[i]=mi;
         if(s[m][i] >0){      if(mi==0){
           if (s[m][i] >= nlstate+1) {        nbwarn++;
             if(agedc[i]>0)        if(first==0){
               if(moisdc[i]!=99 && andc[i]!=9999)          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                 agev[m][i]=agedc[i];          first=1;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        }
            else {        if(first==1){
               if (andc[i]!=9999){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        }
               agev[m][i]=-1;      } /* end mi==0 */
               }    } /* End individuals */
             }  
           }    for(i=1; i<=imx; i++){
           else if(s[m][i] !=9){ /* Should no more exist */      for(mi=1; mi<wav[i];mi++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        if (stepm <=0)
             if(mint[m][i]==99 || anint[m][i]==9999)          dh[mi][i]=1;
               agev[m][i]=1;        else{
             else if(agev[m][i] <agemin){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
               agemin=agev[m][i];            if (agedc[i] < 2*AGESUP) {
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             }              if(j==0) j=1;  /* Survives at least one month after exam */
             else if(agev[m][i] >agemax){              else if(j<0){
               agemax=agev[m][i];                nberr++;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }                j=1; /* Temporary Dangerous patch */
             /*agev[m][i]=anint[m][i]-annais[i];*/                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);
             /*   agev[m][i] = age[i]+2*m;*/                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           else { /* =9 */              }
             agev[m][i]=1;              k=k+1;
             s[m][i]=-1;              if (j >= jmax){
           }                jmax=j;
         }                ijmax=i;
         else /*= 0 Unknown */              }
           agev[m][i]=1;              if (j <= jmin){
       }                jmin=j;
                    ijmin=i;
     }              }
     for (i=1; i<=imx; i++)  {              sum=sum+j;
       for(m=1; (m<= maxwav); m++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         if (s[m][i] > (nlstate+ndeath)) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           printf("Error: Wrong value in nlstate or ndeath\n");              }
           goto end;          }
         }          else{
       }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     }  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            k=k+1;
             if (j >= jmax) {
     free_vector(severity,1,maxwav);              jmax=j;
     free_imatrix(outcome,1,maxwav+1,1,n);              ijmax=i;
     free_vector(moisnais,1,n);            }
     free_vector(annais,1,n);            else if (j <= jmin){
     /* free_matrix(mint,1,maxwav,1,n);              jmin=j;
        free_matrix(anint,1,maxwav,1,n);*/              ijmin=i;
     free_vector(moisdc,1,n);            }
     free_vector(andc,1,n);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                if(j<0){
     wav=ivector(1,imx);              nberr++;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              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]);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              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]);
                }
     /* Concatenates waves */            sum=sum+j;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          }
           jk= j/stepm;
           jl= j -jk*stepm;
       Tcode=ivector(1,100);          ju= j -(jk+1)*stepm;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       ncodemax[1]=1;            if(jl==0){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              dh[mi][i]=jk;
                    bh[mi][i]=0;
    codtab=imatrix(1,100,1,10);            }else{ /* We want a negative bias in order to only have interpolation ie
    h=0;                    * to avoid the price of an extra matrix product in likelihood */
    m=pow(2,cptcoveff);              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
    for(k=1;k<=cptcoveff; k++){            }
      for(i=1; i <=(m/pow(2,k));i++){          }else{
        for(j=1; j <= ncodemax[k]; j++){            if(jl <= -ju){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              dh[mi][i]=jk;
            h++;              bh[mi][i]=jl;       /* bias is positive if real duration
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                                   * is higher than the multiple of stepm and negative otherwise.
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                                   */
          }            }
        }            else{
      }              dh[mi][i]=jk+1;
    }              bh[mi][i]=ju;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            }
       codtab[1][2]=1;codtab[2][2]=2; */            if(dh[mi][i]==0){
    /* for(i=1; i <=m ;i++){              dh[mi][i]=1; /* At least one step */
       for(k=1; k <=cptcovn; k++){              bh[mi][i]=ju; /* At least one step */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
       }            }
       printf("\n");          } /* end if mle */
       }        }
       scanf("%d",i);*/      } /* end wave */
        }
    /* Calculates basic frequencies. Computes observed prevalence at single age    jmean=sum/k;
        and prints on file fileres'p'. */    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
       }
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*********** Tricode ****************************/
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  {
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
           * Boring subroutine which should only output nbcode[Tvar[j]][k]
     /* For Powell, parameters are in a vector p[] starting at p[1]     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */     * nbcode[Tvar[j]][1]= 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    */
   
     if(mle==1){    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    int modmaxcovj=0; /* Modality max of covariates j */
     }    int cptcode=0; /* Modality max of covariates j */
        int modmincovj=0; /* Modality min of covariates j */
     /*--------- 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);  
      cptcoveff=0; 
    
    jk=1;    for (k=-1; k < maxncov; k++) Ndum[k]=0;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    for(i=1,jk=1; i <=nlstate; i++){    /* Loop on covariates without age and products */
      for(k=1; k <=(nlstate+ndeath); k++){    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
        if (k != i)      for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
          {                                 modality of this covariate Vj*/ 
            printf("%d%d ",i,k);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
            fprintf(ficres,"%1d%1d ",i,k);                                      * If product of Vn*Vm, still boolean *:
            for(j=1; j <=ncovmodel; j++){                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
              printf("%f ",p[jk]);                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
              fprintf(ficres,"%f ",p[jk]);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
              jk++;                                        modality of the nth covariate of individual i. */
            }        if (ij > modmaxcovj)
            printf("\n");          modmaxcovj=ij; 
            fprintf(ficres,"\n");        else if (ij < modmincovj) 
          }          modmincovj=ij; 
      }        if ((ij < -1) && (ij > NCOVMAX)){
    }          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
  if(mle==1){          exit(1);
     /* Computing hessian and covariance matrix */        }else
     ftolhess=ftol; /* Usually correct */        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     hesscov(matcov, p, npar, delti, ftolhess, func);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
  }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        /* getting the maximum value of the modality of the covariate
     printf("# Scales (for hessian or gradient estimation)\n");           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
      for(i=1,jk=1; i <=nlstate; i++){           female is 1, then modmaxcovj=1.*/
       for(j=1; j <=nlstate+ndeath; j++){      } /* end for loop on individuals */
         if (j!=i) {      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
           fprintf(ficres,"%1d%1d",i,j);      cptcode=modmaxcovj;
           printf("%1d%1d",i,j);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
           for(k=1; k<=ncovmodel;k++){     /*for (i=0; i<=cptcode; i++) {*/
             printf(" %.5e",delti[jk]);      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
             fprintf(ficres," %.5e",delti[jk]);        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
             jk++;        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           }          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
           printf("\n");        }
           fprintf(ficres,"\n");        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
         }           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       }      } /* Ndum[-1] number of undefined modalities */
      }  
          /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     k=1;      /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
     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 Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
     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");         modmincovj=3; modmaxcovj = 7;
     for(i=1;i<=npar;i++){         There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
       /*  if (k>nlstate) k=1;         which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
       i1=(i-1)/(ncovmodel*nlstate)+1;         defining two dummy variables: variables V1_1 and V1_2.
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);         nbcode[Tvar[j]][ij]=k;
       printf("%s%d%d",alph[k],i1,tab[i]);*/         nbcode[Tvar[j]][1]=0;
       fprintf(ficres,"%3d",i);         nbcode[Tvar[j]][2]=1;
       printf("%3d",i);         nbcode[Tvar[j]][3]=2;
       for(j=1; j<=i;j++){      */
         fprintf(ficres," %.5e",matcov[i][j]);      ij=1; /* ij is similar to i but can jumps over null modalities */
         printf(" %.5e",matcov[i][j]);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
       }        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
       fprintf(ficres,"\n");          /*recode from 0 */
       printf("\n");          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
       k++;            nbcode[Tvar[j]][ij]=k;  /* stores the modality k in an array nbcode. 
     }                                       k is a modality. If we have model=V1+V1*sex 
                                           then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     while((c=getc(ficpar))=='#' && c!= EOF){            ij++;
       ungetc(c,ficpar);          }
       fgets(line, MAXLINE, ficpar);          if (ij > ncodemax[j]) break; 
       puts(line);        }  /* end of loop on */
       fputs(line,ficparo);      } /* end of loop on modality */ 
     }    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     ungetc(c,ficpar);    
     estepm=0;   for (k=-1; k< maxncov; k++) Ndum[k]=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;    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
     if (fage <= 2) {     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
       bage = ageminpar;     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
       fage = agemaxpar;     Ndum[ij]++; /* Might be supersed V1 + V1*age */
     }   } 
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");   ij=1;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
       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*/
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);  
   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);  
        
   while((c=getc(ficpar))=='#' && c!= EOF){  /*********** Health Expectancies ****************/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     puts(line);  
     fputs(line,ficparo);  {
   }    /* Health expectancies, no variances */
   ungetc(c,ficpar);    int i, j, nhstepm, hstepm, h, nstepm;
      int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    double ***p3mat;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    double eip;
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    pstamp(ficreseij);
   fprintf(ficparo,"pop_based=%d\n",popbased);      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   fprintf(ficres,"pop_based=%d\n",popbased);      fprintf(ficreseij,"# Age");
      for(i=1; i<=nlstate;i++){
   while((c=getc(ficpar))=='#' && c!= EOF){      for(j=1; j<=nlstate;j++){
     ungetc(c,ficpar);        fprintf(ficreseij," e%1d%1d ",i,j);
     fgets(line, MAXLINE, ficpar);      }
     puts(line);      fprintf(ficreseij," e%1d. ",i);
     fputs(line,ficparo);    }
   }    fprintf(ficreseij,"\n");
   ungetc(c,ficpar);  
     
   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);    if(estepm < stepm){
 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);      printf ("Problem %d lower than %d\n",estepm, stepm);
 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);    }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
 while((c=getc(ficpar))=='#' && c!= EOF){     * This is mainly to measure the difference between two models: for example
     ungetc(c,ficpar);     * if stepm=24 months pijx are given only every 2 years and by summing them
     fgets(line, MAXLINE, ficpar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     puts(line);     * progression in between and thus overestimating or underestimating according
     fputs(line,ficparo);     * to the curvature of the survival function. If, for the same date, we 
   }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   ungetc(c,ficpar);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);     * curvature will be obtained if estepm is as small as stepm. */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    /* 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. 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
 /*------------ gnuplot -------------*/       Look at hpijx to understand the reason of that which relies in memory size
   strcpy(optionfilegnuplot,optionfilefiname);       and note for a fixed period like estepm months */
   strcat(optionfilegnuplot,".gp");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       survival function given by stepm (the optimization length). Unfortunately it
     printf("Problem with file %s",optionfilegnuplot);       means that if the survival funtion is printed only each two years of age and if
   }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   fclose(ficgp);       results. So we changed our mind and took the option of the best precision.
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    */
 /*--------- index.htm --------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
   strcpy(optionfilehtm,optionfile);    agelim=AGESUP;
   strcat(optionfilehtm,".htm");    /* If stepm=6 months */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     printf("Problem with %s \n",optionfilehtm), exit(0);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   }      
   /* nhstepm age range expressed in number of stepm */
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 \n    /* if (stepm >= YEARM) hstepm=1;*/
 Total number of observations=%d <br>\n    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li>Parameter files<br>\n    for (age=bage; age<=fage; age ++){ 
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fclose(fichtm);      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
        /* If stepm=6 months */
 /*------------ free_vector  -------------*/      /* Computed by stepm unit matrices, product of hstepma matrices, stored
  chdir(path);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
        
  free_ivector(wav,1,imx);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  free_ivector(num,1,n);      
  free_vector(agedc,1,n);      printf("%d|",(int)age);fflush(stdout);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  fclose(ficparo);      
  fclose(ficres);      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   /*--------------- Prevalence limit --------------*/          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
              eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   strcpy(filerespl,"pl");            
   strcat(filerespl,fileres);            /* 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((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          }
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      fprintf(ficreseij,"%3.0f",age );
   fprintf(ficrespl,"#Prevalence limit\n");      for(i=1; i<=nlstate;i++){
   fprintf(ficrespl,"#Age ");        eip=0;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(j=1; j<=nlstate;j++){
   fprintf(ficrespl,"\n");          eip +=eij[i][j][(int)age];
            fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   prlim=matrix(1,nlstate,1,nlstate);        }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficreseij,"%9.4f", eip );
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficreseij,"\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    }
   k=0;    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   agebase=ageminpar;    printf("\n");
   agelim=agemaxpar;    fprintf(ficlog,"\n");
   ftolpl=1.e-10;    
   i1=cptcoveff;  }
   if (cptcovn < 1){i1=1;}  
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  {
         k=k+1;    /* Covariances of health expectancies eij and of total life expectancies according
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/     to initial status i, ei. .
         fprintf(ficrespl,"\n#******");    */
         for(j=1;j<=cptcoveff;j++)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int nhstepma, nstepma; /* Decreasing with age */
         fprintf(ficrespl,"******\n");    double age, agelim, hf;
            double ***p3matp, ***p3matm, ***varhe;
         for (age=agebase; age<=agelim; age++){    double **dnewm,**doldm;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double *xp, *xm;
           fprintf(ficrespl,"%.0f",age );    double **gp, **gm;
           for(i=1; i<=nlstate;i++)    double ***gradg, ***trgradg;
           fprintf(ficrespl," %.5f", prlim[i][i]);    int theta;
           fprintf(ficrespl,"\n");  
         }    double eip, vip;
       }  
     }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   fclose(ficrespl);    xp=vector(1,npar);
     xm=vector(1,npar);
   /*------------- h Pij x at various ages ------------*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    pstamp(ficresstdeij);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   }    fprintf(ficresstdeij,"# Age");
   printf("Computing pij: result on file '%s' \n", filerespij);    for(i=1; i<=nlstate;i++){
        for(j=1; j<=nlstate;j++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   /*if (stepm<=24) stepsize=2;*/      fprintf(ficresstdeij," e%1d. ",i);
     }
   agelim=AGESUP;    fprintf(ficresstdeij,"\n");
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    pstamp(ficrescveij);
      fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   k=0;    fprintf(ficrescveij,"# Age");
   for(cptcov=1;cptcov<=i1;cptcov++){    for(i=1; i<=nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(j=1; j<=nlstate;j++){
       k=k+1;        cptj= (j-1)*nlstate+i;
         fprintf(ficrespij,"\n#****** ");        for(i2=1; i2<=nlstate;i2++)
         for(j=1;j<=cptcoveff;j++)          for(j2=1; j2<=nlstate;j2++){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            cptj2= (j2-1)*nlstate+i2;
         fprintf(ficrespij,"******\n");            if(cptj2 <= cptj)
                      fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
         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 */    fprintf(ficrescveij,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;    if(estepm < stepm){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        printf ("Problem %d lower than %d\n",estepm, stepm);
           fprintf(ficrespij,"# Age");    }
           for(i=1; i<=nlstate;i++)    else  hstepm=estepm;   
             for(j=1; j<=nlstate+ndeath;j++)    /* We compute the life expectancy from trapezoids spaced every estepm months
               fprintf(ficrespij," %1d-%1d",i,j);     * This is mainly to measure the difference between two models: for example
           fprintf(ficrespij,"\n");     * if stepm=24 months pijx are given only every 2 years and by summing them
            for (h=0; h<=nhstepm; h++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );     * progression in between and thus overestimating or underestimating according
             for(i=1; i<=nlstate;i++)     * to the curvature of the survival function. If, for the same date, we 
               for(j=1; j<=nlstate+ndeath;j++)     * estimate the model with stepm=1 month, we can keep estepm to 24 months
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);     * to compare the new estimate of Life expectancy with the same linear 
             fprintf(ficrespij,"\n");     * hypothesis. A more precise result, taking into account a more precise
              }     * curvature will be obtained if estepm is as small as stepm. */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");    /* For example we decided to compute the life expectancy with the smallest unit */
         }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     }       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fclose(ficrespij);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   /*---------- Forecasting ------------------*/       results. So we changed our mind and took the option of the best precision.
   if((stepm == 1) && (strcmp(model,".")==0)){    */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
   }    /* If stepm=6 months */
   else{    /* nhstepm age range expressed in number of stepm */
     erreur=108;    agelim=AGESUP;
     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);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /*---------- Health expectancies and variances ------------*/    
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(filerest,"t");    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcat(filerest,fileres);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   if((ficrest=fopen(filerest,"w"))==NULL) {    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   }    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   strcpy(filerese,"e");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   strcat(filerese,fileres);      /* if (stepm >= YEARM) hstepm=1;*/
   if((ficreseij=fopen(filerese,"w"))==NULL) {      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }      /* If stepm=6 months */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
  strcpy(fileresv,"v");      
   strcat(fileresv,fileres);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      /* Computing  Variances of health expectancies */
   }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);         decrease memory allocation */
   calagedate=-1;      for(theta=1; theta <=npar; theta++){
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   k=0;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       k=k+1;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       fprintf(ficrest,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)        for(j=1; j<= nlstate; j++){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(i=1; i<=nlstate; i++){
       fprintf(ficrest,"******\n");            for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
       fprintf(ficreseij,"\n#****** ");              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       for(j=1;j<=cptcoveff;j++)            }
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
       fprintf(ficreseij,"******\n");        }
        
       fprintf(ficresvij,"\n#****** ");        for(ij=1; ij<= nlstate*nlstate; ij++)
       for(j=1;j<=cptcoveff;j++)          for(h=0; h<=nhstepm-1; h++){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       fprintf(ficresvij,"******\n");          }
       }/* End theta */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      
       oldm=oldms;savm=savms;      
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        for(h=0; h<=nhstepm-1; h++)
          for(j=1; j<=nlstate*nlstate;j++)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for(theta=1; theta <=npar; theta++)
       oldm=oldms;savm=savms;            trgradg[h][j][theta]=gradg[h][theta][j];
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      
      
        for(ij=1;ij<=nlstate*nlstate;ij++)
          for(ji=1;ji<=nlstate*nlstate;ji++)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          varhe[ij][ji][(int)age] =0.;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       epj=vector(1,nlstate+1);       for(h=0;h<=nhstepm-1;h++){
       for(age=bage; age <=fage ;age++){        for(k=0;k<=nhstepm-1;k++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         if (popbased==1) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1; i<=nlstate;i++)          for(ij=1;ij<=nlstate*nlstate;ij++)
             prlim[i][i]=probs[(int)age][i][k];            for(ji=1;ji<=nlstate*nlstate;ji++)
         }              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
                }
         fprintf(ficrest," %4.0f",age);      }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      /* Computing expectancies */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      for(i=1; i<=nlstate;i++)
           }        for(j=1; j<=nlstate;j++)
           epj[nlstate+1] +=epj[j];          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
         for(i=1, vepp=0.;i <=nlstate;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]);*/
           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(ficresstdeij,"%3.0f",age );
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      for(i=1; i<=nlstate;i++){
         }        eip=0.;
         fprintf(ficrest,"\n");        vip=0.;
       }        for(j=1; j<=nlstate;j++){
     }          eip += eij[i][j][(int)age];
   }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
 free_matrix(mint,1,maxwav,1,n);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     free_vector(weight,1,n);        }
   fclose(ficreseij);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   fclose(ficresvij);      }
   fclose(ficrest);      fprintf(ficresstdeij,"\n");
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);      fprintf(ficrescveij,"%3.0f",age );
        for(i=1; i<=nlstate;i++)
   /*------- Variance limit prevalence------*/          for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
   strcpy(fileresvpl,"vpl");          for(i2=1; i2<=nlstate;i2++)
   strcat(fileresvpl,fileres);            for(j2=1; j2<=nlstate;j2++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {              cptj2= (j2-1)*nlstate+i2;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);              if(cptj2 <= cptj)
     exit(0);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   }            }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        }
       fprintf(ficrescveij,"\n");
   k=0;     
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       k=k+1;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       fprintf(ficresvpl,"\n#****** ");    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       for(j=1;j<=cptcoveff;j++)    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresvpl,"******\n");    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          printf("\n");
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    fprintf(ficlog,"\n");
       oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    free_vector(xm,1,npar);
     }    free_vector(xp,1,npar);
  }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   fclose(ficresvpl);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  /************ Variance ******************/
    void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  {
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /* Variance of health expectancies */
      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
      /* double **newm;*/
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    int movingaverage();
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    double **dnewm,**doldm;
      double **dnewmp,**doldmp;
   free_matrix(matcov,1,npar,1,npar);    int i, j, nhstepm, hstepm, h, nstepm ;
   free_vector(delti,1,npar);    int k;
   free_matrix(agev,1,maxwav,1,imx);    double *xp;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
   fprintf(fichtm,"\n</body>");    double **gradgp, **trgradgp; /* for var p point j */
   fclose(fichtm);    double *gpp, *gmp; /* for var p point j */
   fclose(ficgp);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      double ***p3mat;
     double age,agelim, hf;
   if(erreur >0)    double ***mobaverage;
     printf("End of Imach with error or warning %d\n",erreur);    int theta;
   else   printf("End of Imach\n");    char digit[4];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    char digitp[25];
    
   /* 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);*/    char fileresprobmorprev[FILENAMELENGTH];
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/    if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
  end:      else strcpy(digitp,"-populbased-nomobil-");
 #ifdef windows    }
   /* chdir(pathcd);*/    else 
 #endif      strcpy(digitp,"-stablbased-");
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    if (mobilav!=0) {
  /*system("cd ../gp37mgw");*/      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
  strcpy(plotcmd,GNUPLOTPROGRAM);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  strcat(plotcmd," ");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  strcat(plotcmd,optionfilegnuplot);      }
  system(plotcmd);    }
   
 #ifdef windows    strcpy(fileresprobmorprev,"prmorprev"); 
   while (z[0] != 'q') {    sprintf(digit,"%-d",ij);
     /* chdir(path); */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     scanf("%s",z);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     if (z[0] == 'c') system("./imach");    strcat(fileresprobmorprev,fileres);
     else if (z[0] == 'e') system(optionfilehtm);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     else if (z[0] == 'g') system(plotcmd);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     else if (z[0] == 'q') exit(0);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   }    }
 #endif    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 }   
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           if(nagesqr==1)
             cov[3]= age*age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
     for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficgp,"# initial state %d\n",i);
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           fprintf(ficgp,"#   current state %d\n",k);
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
             jk++; 
           }
           fprintf(ficgp,"\n");
         }
       }
      }
     fprintf(ficgp,"##############\n#\n");
   
     /*goto avoid;*/
     fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
     fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
     fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
     fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
     fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
     fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
     fprintf(ficgp,"#\n");
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        fprintf(ficgp,"# ng=%d\n",ng);
        fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"#    jk=%d\n",jk);
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  if(nagesqr==0)
                    fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                else
                  if(nagesqr==0)
                    fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel-nagesqr; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){ 
                  if(nagesqr==0)
                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
     
                  ij=1;
                  for(j=3; j <=ncovmodel-nagesqr; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
      * - nagesqr = 1 if age*age in the model, otherwise 0.
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
      * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
     char *strpt;
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       strcpy(modelsav,model); 
       if ((strpt=strstr(model,"age*age")) !=0){
         printf(" strpt=%s, model=%s\n",strpt, model);
         if(strpt != model){
         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
    corresponding column of parameters.\n",model);
         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \
    corresponding column of parameters.\n",model); fflush(ficlog);
         return 1;
       }
   
         nagesqr=1;
         if (strstr(model,"+age*age") !=0)
           substrchaine(modelsav, model, "+age*age");
         else if (strstr(model,"age*age+") !=0)
           substrchaine(modelsav, model, "age*age+");
         else 
           substrchaine(modelsav, model, "age*age");
       }else
         nagesqr=0;
       if (strlen(modelsav) >1){
         j=nbocc(modelsav,'+'); /**< j=Number of '+' */
         j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
         cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
         cptcovt= j+1; /* Number of total covariates in the model, not including
                      * cst, age and age*age 
                      * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated 
                     * separately: ncovn=4- 2=2 (V1+V3). */
         cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
         cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
   
       
         /*   Design
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
          *  <          ncovcol=8                >
          * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
          *   k=  1    2      3       4     5       6      7        8
          *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
          *  covar[k,i], value of kth covariate if not including age for individual i:
          *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
          *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
          *  Tage[++cptcovage]=k
          *       if products, new covar are created after ncovcol with k1
          *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
          *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
          *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
          *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
          *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
          *  <          ncovcol=8                >
          *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
          *          k=  1    2      3       4     5       6      7        8    9   10   11  12
          *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
          * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          * p Tprod[1]@2={                         6, 5}
          *p Tvard[1][1]@4= {7, 8, 5, 6}
          * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
          *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          *How to reorganize?
          * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
          * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          *       {2,   1,     4,      8,    5,      6,     3,       7}
          * Struct []
          */
   
         /* This loop fills the array Tvar from the string 'model'.*/
         /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
         /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
         /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
         /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
         /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
         /*        k=1 Tvar[1]=2 (from V2) */
         /*        k=5 Tvar[5] */
         /* for (k=1; k<=cptcovn;k++) { */
         /*        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
         /*        } */
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
         /*
          * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
         for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
         cptcovage=0;
         for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                            modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
           if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
           /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
           /*scanf("%d",i);*/
           if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
             cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
             if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
               /* covar is not filled and then is empty */
               cptcovprod--;
               cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
               Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
               cptcovage++; /* Sums the number of covariates which include age as a product */
               Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
               /*printf("stre=%s ", stre);*/
             } else if (strcmp(strd,"age")==0) { /* or age*Vn */
               cptcovprod--;
               cutl(stre,strb,strc,'V');
               Tvar[k]=atoi(stre);
               cptcovage++;
               Tage[cptcovage]=k;
             } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
               /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
               cptcovn++;
               cptcovprodnoage++;k1++;
               cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
               Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                      because this model-covariate is a construction we invent a new column
                                      ncovcol + k1
                                      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                      Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
               cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
               Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
               Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
               Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
               k2=k2+2;
               Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
               Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
               for (i=1; i<=lastobs;i++){
                 /* Computes the new covariate which is a product of
                    covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                 covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
               }
             } /* End age is not in the model */
           } /* End if model includes a product */
           else { /* no more sum */
             /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
             /*  scanf("%d",i);*/
             cutl(strd,strc,strb,'V');
             ks++; /**< Number of simple covariates */
             cptcovn++;
             Tvar[k]=atoi(strd);
           }
           strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
           /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
             scanf("%d",i);*/
         } /* end of loop + on total covariates */
       } /* end if strlen(modelsave == 0) age*age might exist */
     } /* end if strlen(model == 0) */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           return 0;
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
           return 0;
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Main Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /* Main ---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
       model[strlen(model)-1]='\0';
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     /* if(model[0]=='#'|| model[0]== '\0'){ */
     if(model[0]=='#'){
       printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
    'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
    'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
       if(mle != -1){
         printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
         exit(1);
       }
     }
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
     else
       ncovmodel=2; /* Constant and age */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) { /* Main Wizard */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*  Main data
      */
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
   /* Main decodemodel */
   
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] is the maximum value of this jth covariate */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              * For k=4 covariates, h goes from 1 to 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
              *     h\k   1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /* codtab[12][3]=1; */
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /* Initialisation of ----------- gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
   
   
     /* Initialisation of --------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
       /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
       /*     gsl_vector_set(x, 0, 0.0268); */
       /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 mortality only */
     /* Standard maximisation */
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* again, to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%12.7f ",p[jk]);
               fprintf(ficlog,"%12.7f ",p[jk]);
               fprintf(ficres,"%12.7f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   
       /* Other stuffs, more or less useful */    
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /* Other results (useful)*/
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
    
       /* ------ Other prevalence ratios------------ */
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(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.1.47  
changed lines
  Added in v.1.190


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