Diff for /imach/src/imach.c between versions 1.25 and 1.183

version 1.25, 2002/02/26 17:11:54 version 1.183, 2015/03/10 20:34:32
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.183  2015/03/10 20:34:32  brouard
      Summary: 0.98q0, trying with directest, mnbrak fixed
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    We use directest instead of original Powell test; probably no
   first survey ("cross") where individuals from different ages are    incidence on the results, but better justifications;
   interviewed on their health status or degree of disability (in the    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   case of a health survey which is our main interest) -2- at least a    wrong results.
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.182  2015/02/12 08:19:57  brouard
   computed from the time spent in each health state according to a    Summary: Trying to keep directest which seems simpler and more general
   model. More health states you consider, more time is necessary to reach the    Author: Nicolas Brouard
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.181  2015/02/11 23:22:24  brouard
   probabibility to be observed in state j at the second wave    Summary: Comments on Powell added
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Author:
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.180  2015/02/11 17:33:45  brouard
   where the markup *Covariates have to be included here again* invites    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.179  2015/01/04 09:57:06  brouard
     Summary: back to OS/X
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.178  2015/01/04 09:35:48  brouard
   identical for each individual. Also, if a individual missed an    *** empty log message ***
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.177  2015/01/03 18:40:56  brouard
     Summary: Still testing ilc32 on OSX
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.176  2015/01/03 16:45:04  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    *** empty log message ***
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.175  2015/01/03 16:33:42  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    *** empty log message ***
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.174  2015/01/03 16:15:49  brouard
     Summary: Still in cross-compilation
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.173  2015/01/03 12:06:26  brouard
      Summary: trying to detect cross-compilation
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.172  2014/12/27 12:07:47  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.171  2014/12/23 13:26:59  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: Back from Visual C
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Still problem with utsname.h on Windows
    
 #include <math.h>    Revision 1.170  2014/12/23 11:17:12  brouard
 #include <stdio.h>    Summary: Cleaning some \%% back to %%
 #include <stdlib.h>  
 #include <unistd.h>    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
 #define MAXLINE 256    Revision 1.169  2014/12/22 23:08:31  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Summary: 0.98p
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.168  2014/12/22 15:17:42  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Summary: update
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.167  2014/12/22 13:50:56  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: Testing uname and compiler version and if compiled 32 or 64
   
 #define NINTERVMAX 8    Testing on Linux 64
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.166  2014/12/22 11:40:47  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    *** empty log message ***
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.165  2014/12/16 11:20:36  brouard
 #define AGESUP 130    Summary: After compiling on Visual C
 #define AGEBASE 40  
     * imach.c (Module): Merging 1.61 to 1.162
   
 int erreur; /* Error number */    Revision 1.164  2014/12/16 10:52:11  brouard
 int nvar;    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    * imach.c (Module): Merging 1.61 to 1.162
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.163  2014/12/16 10:30:11  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * imach.c (Module): Merging 1.61 to 1.162
 int popbased=0;  
     Revision 1.162  2014/09/25 11:43:39  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Summary: temporary backup 0.99!
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.1  2014/09/16 11:06:58  brouard
 int mle, weightopt;    Summary: With some code (wrong) for nlopt
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Author:
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.161  2014/09/15 20:41:41  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Summary: Problem with macro SQR on Intel compiler
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.160  2014/09/02 09:24:05  brouard
 FILE *ficreseij;    *** empty log message ***
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.159  2014/09/01 10:34:10  brouard
   char fileresv[FILENAMELENGTH];    Summary: WIN32
  FILE  *ficresvpl;    Author: Brouard
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.158  2014/08/27 17:11:51  brouard
 #define NR_END 1    *** empty log message ***
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.157  2014/08/27 16:26:55  brouard
     Summary: Preparing windows Visual studio version
 #define NRANSI    Author: Brouard
 #define ITMAX 200  
     In order to compile on Visual studio, time.h is now correct and time_t
 #define TOL 2.0e-4    and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
 #define CGOLD 0.3819660    Trying to suppress #ifdef LINUX
 #define ZEPS 1.0e-10    Add xdg-open for __linux in order to open default browser.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.156  2014/08/25 20:10:10  brouard
 #define GOLD 1.618034    *** empty log message ***
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
 static double maxarg1,maxarg2;    Author: Brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.154  2014/06/20 17:32:08  brouard
      Summary: Outputs now all graphs of convergence to period prevalence
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
 static double sqrarg;    Author: Brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.152  2014/06/18 17:54:09  brouard
     Summary: open browser, use gnuplot on same dir than imach if not found in the path
 int imx;  
 int stepm;    Revision 1.151  2014/06/18 16:43:30  brouard
 /* Stepm, step in month: minimum step interpolation*/    *** empty log message ***
   
 int m,nb;    Revision 1.150  2014/06/18 16:42:35  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Author: brouard
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.149  2014/06/18 15:51:14  brouard
     Summary: Some fixes in parameter files errors
 double *weight;    Author: Nicolas Brouard
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.148  2014/06/17 17:38:48  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Summary: Nothing new
     Author: Brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Just a new packaging for OS/X version 0.98nS
   
 /**************** split *************************/    Revision 1.147  2014/06/16 10:33:11  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    *** empty log message ***
 {  
    char *s;                             /* pointer */    Revision 1.146  2014/06/16 10:20:28  brouard
    int  l1, l2;                         /* length counters */    Summary: Merge
     Author: Brouard
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Merge, before building revised version.
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.145  2014/06/10 21:23:15  brouard
 #else    Summary: Debugging with valgrind
    s = strrchr( path, '/' );            /* find last / */    Author: Nicolas Brouard
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Lot of changes in order to output the results with some covariates
 #if     defined(__bsd__)                /* get current working directory */    After the Edimburgh REVES conference 2014, it seems mandatory to
       extern char       *getwd( );    improve the code.
     No more memory valgrind error but a lot has to be done in order to
       if ( getwd( dirc ) == NULL ) {    continue the work of splitting the code into subroutines.
 #else    Also, decodemodel has been improved. Tricode is still not
       extern char       *getcwd( );    optimal. nbcode should be improved. Documentation has been added in
     the source code.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.143  2014/01/26 09:45:38  brouard
          return( GLOCK_ERROR_GETCWD );    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
       }  
       strcpy( name, path );             /* we've got it */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    } else {                             /* strip direcotry from path */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.142  2014/01/26 03:57:36  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.141  2014/01/26 02:42:01  brouard
    l1 = strlen( dirc );                 /* length of directory */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.140  2011/09/02 10:37:54  brouard
 #else    Summary: times.h is ok with mingw32 now.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.139  2010/06/14 07:50:17  brouard
    s = strrchr( name, '.' );            /* find last / */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
    s++;    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.138  2010/04/30 18:19:40  brouard
    l2= strlen( s)+1;    *** empty log message ***
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.137  2010/04/29 18:11:38  brouard
    return( 0 );                         /* we're done */    (Module): Checking covariates for more complex models
 }    than V1+V2. A lot of change to be done. Unstable.
   
     Revision 1.136  2010/04/26 20:30:53  brouard
 /******************************************/    (Module): merging some libgsl code. Fixing computation
     of likelione (using inter/intrapolation if mle = 0) in order to
 void replace(char *s, char*t)    get same likelihood as if mle=1.
 {    Some cleaning of code and comments added.
   int i;  
   int lg=20;    Revision 1.135  2009/10/29 15:33:14  brouard
   i=0;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.134  2009/10/29 13:18:53  brouard
     (s[i] = t[i]);    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.133  2009/07/06 10:21:25  brouard
 }    just nforces
   
 int nbocc(char *s, char occ)    Revision 1.132  2009/07/06 08:22:05  brouard
 {    Many tings
   int i,j=0;  
   int lg=20;    Revision 1.131  2009/06/20 16:22:47  brouard
   i=0;    Some dimensions resccaled
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.130  2009/05/26 06:44:34  brouard
   if  (s[i] == occ ) j++;    (Module): Max Covariate is now set to 20 instead of 8. A
   }    lot of cleaning with variables initialized to 0. Trying to make
   return j;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 }  
     Revision 1.129  2007/08/31 13:49:27  lievre
 void cutv(char *u,char *v, char*t, char occ)    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 {  
   int i,lg,j,p=0;    Revision 1.128  2006/06/30 13:02:05  brouard
   i=0;    (Module): Clarifications on computing e.j
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    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
   lg=strlen(t);    loop. Now we define nhstepma in the age loop.
   for(j=0; j<p; j++) {    (Module): In order to speed up (in case of numerous covariates) we
     (u[j] = t[j]);    compute health expectancies (without variances) in a first step
   }    and then all the health expectancies with variances or standard
      u[p]='\0';    deviation (needs data from the Hessian matrices) which slows the
     computation.
    for(j=0; j<= lg; j++) {    In the future we should be able to stop the program is only health
     if (j>=(p+1))(v[j-p-1] = t[j]);    expectancies and graph are needed without standard deviations.
   }  
 }    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
 /********************** nrerror ********************/    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 void nrerror(char error_text[])    Version 0.98h
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.125  2006/04/04 15:20:31  lievre
   fprintf(stderr,"%s\n",error_text);    Errors in calculation of health expectancies. Age was not initialized.
   exit(1);    Forecasting file added.
 }  
 /*********************** vector *******************/    Revision 1.124  2006/03/22 17:13:53  lievre
 double *vector(int nl, int nh)    Parameters are printed with %lf instead of %f (more numbers after the comma).
 {    The log-likelihood is printed in the log file
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.123  2006/03/20 10:52:43  brouard
   if (!v) nrerror("allocation failure in vector");    * imach.c (Module): <title> changed, corresponds to .htm file
   return v-nl+NR_END;    name. <head> headers where missing.
 }  
     * imach.c (Module): Weights can have a decimal point as for
 /************************ free vector ******************/    English (a comma might work with a correct LC_NUMERIC environment,
 void free_vector(double*v, int nl, int nh)    otherwise the weight is truncated).
 {    Modification of warning when the covariates values are not 0 or
   free((FREE_ARG)(v+nl-NR_END));    1.
 }    Version 0.98g
   
 /************************ivector *******************************/    Revision 1.122  2006/03/20 09:45:41  brouard
 int *ivector(long nl,long nh)    (Module): Weights can have a decimal point as for
 {    English (a comma might work with a correct LC_NUMERIC environment,
   int *v;    otherwise the weight is truncated).
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Modification of warning when the covariates values are not 0 or
   if (!v) nrerror("allocation failure in ivector");    1.
   return v-nl+NR_END;    Version 0.98g
 }  
     Revision 1.121  2006/03/16 17:45:01  lievre
 /******************free ivector **************************/    * imach.c (Module): Comments concerning covariates added
 void free_ivector(int *v, long nl, long nh)  
 {    * imach.c (Module): refinements in the computation of lli if
   free((FREE_ARG)(v+nl-NR_END));    status=-2 in order to have more reliable computation if stepm is
 }    not 1 month. Version 0.98f
   
 /******************* imatrix *******************************/    Revision 1.120  2006/03/16 15:10:38  lievre
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Module): refinements in the computation of lli if
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    status=-2 in order to have more reliable computation if stepm is
 {    not 1 month. Version 0.98f
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.119  2006/03/15 17:42:26  brouard
      (Module): Bug if status = -2, the loglikelihood was
   /* allocate pointers to rows */    computed as likelihood omitting the logarithm. Version O.98e
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.118  2006/03/14 18:20:07  brouard
   m += NR_END;    (Module): varevsij Comments added explaining the second
   m -= nrl;    table of variances if popbased=1 .
      (Module): Covariances of eij, ekl added, graphs fixed, new html link.
      (Module): Function pstamp added
   /* allocate rows and set pointers to them */    (Module): Version 0.98d
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.117  2006/03/14 17:16:22  brouard
   m[nrl] += NR_END;    (Module): varevsij Comments added explaining the second
   m[nrl] -= ncl;    table of variances if popbased=1 .
      (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): Function pstamp added
      (Module): Version 0.98d
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.116  2006/03/06 10:29:27  brouard
 }    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.115  2006/02/27 12:17:45  brouard
       int **m;    (Module): One freematrix added in mlikeli! 0.98c
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.114  2006/02/26 12:57:58  brouard
 {    (Module): Some improvements in processing parameter
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    filename with strsep.
   free((FREE_ARG) (m+nrl-NR_END));  
 }    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 /******************* matrix *******************************/    datafile was not closed, some imatrix were not freed and on matrix
 double **matrix(long nrl, long nrh, long ncl, long nch)    allocation too.
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Revision 1.112  2006/01/30 09:55:26  brouard
   double **m;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.111  2006/01/25 20:38:18  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Lots of cleaning and bugs added (Gompertz)
   m += NR_END;    (Module): Comments can be added in data file. Missing date values
   m -= nrl;    can be a simple dot '.'.
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.110  2006/01/25 00:51:50  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Lots of cleaning and bugs added (Gompertz)
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.108  2006/01/19 18:05:42  lievre
 }    Gnuplot problem appeared...
     To be fixed
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Revision 1.107  2006/01/19 16:20:37  brouard
 {    Test existence of gnuplot in imach path
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.106  2006/01/19 13:24:36  brouard
 }    Some cleaning and links added in html output
   
 /******************* ma3x *******************************/    Revision 1.105  2006/01/05 20:23:19  lievre
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    *** empty log message ***
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.104  2005/09/30 16:11:43  lievre
   double ***m;    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    that the person is alive, then we can code his/her status as -2
   if (!m) nrerror("allocation failure 1 in matrix()");    (instead of missing=-1 in earlier versions) and his/her
   m += NR_END;    contributions to the likelihood is 1 - Prob of dying from last
   m -= nrl;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.103  2005/09/30 15:54:49  lievre
   m[nrl] += NR_END;    (Module): sump fixed, loop imx fixed, and simplifications.
   m[nrl] -= ncl;  
     Revision 1.102  2004/09/15 17:31:30  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Add the possibility to read data file including tab characters.
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Revision 1.101  2004/09/15 10:38:38  brouard
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Fix on curr_time
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Revision 1.100  2004/07/12 18:29:06  brouard
   for (j=ncl+1; j<=nch; j++)    Add version for Mac OS X. Just define UNIX in Makefile
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Revision 1.99  2004/06/05 08:57:40  brouard
   for (i=nrl+1; i<=nrh; i++) {    *** empty log message ***
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.98  2004/05/16 15:05:56  brouard
       m[i][j]=m[i][j-1]+nlay;    New version 0.97 . First attempt to estimate force of mortality
   }    directly from the data i.e. without the need of knowing the health
   return m;    state at each age, but using a Gompertz model: log u =a + b*age .
 }    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 /*************************free ma3x ************************/    cross-longitudinal survey is different from the mortality estimated
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    from other sources like vital statistic data.
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    The same imach parameter file can be used but the option for mle should be -3.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Agnès, who wrote this part of the code, tried to keep most of the
 }    former routines in order to include the new code within the former code.
   
 /***************** f1dim *************************/    The output is very simple: only an estimate of the intercept and of
 extern int ncom;    the slope with 95% confident intervals.
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    Current limitations:
      A) Even if you enter covariates, i.e. with the
 double f1dim(double x)    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 {    B) There is no computation of Life Expectancy nor Life Table.
   int j;  
   double f;    Revision 1.97  2004/02/20 13:25:42  lievre
   double *xt;    Version 0.96d. Population forecasting command line is (temporarily)
      suppressed.
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Revision 1.96  2003/07/15 15:38:55  brouard
   f=(*nrfunc)(xt);    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   free_vector(xt,1,ncom);    rewritten within the same printf. Workaround: many printfs.
   return f;  
 }    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 /*****************brent *************************/    (Repository): Using imachwizard code to output a more meaningful covariance
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    matrix (cov(a12,c31) instead of numbers.
 {  
   int iter;    Revision 1.94  2003/06/27 13:00:02  brouard
   double a,b,d,etemp;    Just cleaning
   double fu,fv,fw,fx;  
   double ftemp;    Revision 1.93  2003/06/25 16:33:55  brouard
   double p,q,r,tol1,tol2,u,v,w,x,xm;    (Module): On windows (cygwin) function asctime_r doesn't
   double e=0.0;    exist so I changed back to asctime which exists.
      (Module): Version 0.96b
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    Revision 1.92  2003/06/25 16:30:45  brouard
   x=w=v=bx;    (Module): On windows (cygwin) function asctime_r doesn't
   fw=fv=fx=(*f)(x);    exist so I changed back to asctime which exists.
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    Revision 1.91  2003/06/25 15:30:29  brouard
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    * imach.c (Repository): Duplicated warning errors corrected.
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    (Repository): Elapsed time after each iteration is now output. It
     printf(".");fflush(stdout);    helps to forecast when convergence will be reached. Elapsed time
 #ifdef DEBUG    is stamped in powell.  We created a new html file for the graphs
     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);    concerning matrix of covariance. It has extension -cov.htm.
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    Revision 1.90  2003/06/24 12:34:15  brouard
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    (Module): Some bugs corrected for windows. Also, when
       *xmin=x;    mle=-1 a template is output in file "or"mypar.txt with the design
       return fx;    of the covariance matrix to be input.
     }  
     ftemp=fu;    Revision 1.89  2003/06/24 12:30:52  brouard
     if (fabs(e) > tol1) {    (Module): Some bugs corrected for windows. Also, when
       r=(x-w)*(fx-fv);    mle=-1 a template is output in file "or"mypar.txt with the design
       q=(x-v)*(fx-fw);    of the covariance matrix to be input.
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);    Revision 1.88  2003/06/23 17:54:56  brouard
       if (q > 0.0) p = -p;    * 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.
       q=fabs(q);  
       etemp=e;    Revision 1.87  2003/06/18 12:26:01  brouard
       e=d;    Version 0.96
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    Revision 1.86  2003/06/17 20:04:08  brouard
       else {    (Module): Change position of html and gnuplot routines and added
         d=p/q;    routine fileappend.
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)    Revision 1.85  2003/06/17 13:12:43  brouard
           d=SIGN(tol1,xm-x);    * imach.c (Repository): Check when date of death was earlier that
       }    current date of interview. It may happen when the death was just
     } else {    prior to the death. In this case, dh was negative and likelihood
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    was wrong (infinity). We still send an "Error" but patch by
     }    assuming that the date of death was just one stepm after the
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    interview.
     fu=(*f)(u);    (Repository): Because some people have very long ID (first column)
     if (fu <= fx) {    we changed int to long in num[] and we added a new lvector for
       if (u >= x) a=x; else b=x;    memory allocation. But we also truncated to 8 characters (left
       SHFT(v,w,x,u)    truncation)
         SHFT(fv,fw,fx,fu)    (Repository): No more line truncation errors.
         } else {  
           if (u < x) a=u; else b=u;    Revision 1.84  2003/06/13 21:44:43  brouard
           if (fu <= fw || w == x) {    * imach.c (Repository): Replace "freqsummary" at a correct
             v=w;    place. It differs from routine "prevalence" which may be called
             w=u;    many times. Probs is memory consuming and must be used with
             fv=fw;    parcimony.
             fw=fu;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
           } else if (fu <= fv || v == x || v == w) {  
             v=u;    Revision 1.83  2003/06/10 13:39:11  lievre
             fv=fu;    *** empty log message ***
           }  
         }    Revision 1.82  2003/06/05 15:57:20  brouard
   }    Add log in  imach.c and  fullversion number is now printed.
   nrerror("Too many iterations in brent");  
   *xmin=x;  */
   return fx;  /*
 }     Interpolated Markov Chain
   
 /****************** mnbrak ***********************/    Short summary of the programme:
     
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    This program computes Healthy Life Expectancies from
             double (*func)(double))    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 {    first survey ("cross") where individuals from different ages are
   double ulim,u,r,q, dum;    interviewed on their health status or degree of disability (in the
   double fu;    case of a health survey which is our main interest) -2- at least a
      second wave of interviews ("longitudinal") which measure each change
   *fa=(*func)(*ax);    (if any) in individual health status.  Health expectancies are
   *fb=(*func)(*bx);    computed from the time spent in each health state according to a
   if (*fb > *fa) {    model. More health states you consider, more time is necessary to reach the
     SHFT(dum,*ax,*bx,dum)    Maximum Likelihood of the parameters involved in the model.  The
       SHFT(dum,*fb,*fa,dum)    simplest model is the multinomial logistic model where pij is the
       }    probability to be observed in state j at the second wave
   *cx=(*bx)+GOLD*(*bx-*ax);    conditional to be observed in state i at the first wave. Therefore
   *fc=(*func)(*cx);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   while (*fb > *fc) {    'age' is age and 'sex' is a covariate. If you want to have a more
     r=(*bx-*ax)*(*fb-*fc);    complex model than "constant and age", you should modify the program
     q=(*bx-*cx)*(*fb-*fa);    where the markup *Covariates have to be included here again* invites
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    you to do it.  More covariates you add, slower the
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    convergence.
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {    The advantage of this computer programme, compared to a simple
       fu=(*func)(u);    multinomial logistic model, is clear when the delay between waves is not
     } else if ((*cx-u)*(u-ulim) > 0.0) {    identical for each individual. Also, if a individual missed an
       fu=(*func)(u);    intermediate interview, the information is lost, but taken into
       if (fu < *fc) {    account using an interpolation or extrapolation.  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    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
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    split into an exact number (nh*stepm) of unobserved intermediate
       u=ulim;    states. This elementary transition (by month, quarter,
       fu=(*func)(u);    semester or year) is modelled as a multinomial logistic.  The hPx
     } else {    matrix is simply the matrix product of nh*stepm elementary matrices
       u=(*cx)+GOLD*(*cx-*bx);    and the contribution of each individual to the likelihood is simply
       fu=(*func)(u);    hPijx.
     }  
     SHFT(*ax,*bx,*cx,u)    Also this programme outputs the covariance matrix of the parameters but also
       SHFT(*fa,*fb,*fc,fu)    of the life expectancies. It also computes the period (stable) prevalence. 
       }    
 }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 /*************** linmin ************************/    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 int ncom;    It is copyrighted identically to a GNU software product, ie programme and
 double *pcom,*xicom;    software can be distributed freely for non commercial use. Latest version
 double (*nrfunc)(double []);    can be accessed at http://euroreves.ined.fr/imach .
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   double brent(double ax, double bx, double cx,    
                double (*f)(double), double tol, double *xmin);    **********************************************************************/
   double f1dim(double x);  /*
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    main
               double *fc, double (*func)(double));    read parameterfile
   int j;    read datafile
   double xx,xmin,bx,ax;    concatwav
   double fx,fb,fa;    freqsummary
      if (mle >= 1)
   ncom=n;      mlikeli
   pcom=vector(1,n);    print results files
   xicom=vector(1,n);    if mle==1 
   nrfunc=func;       computes hessian
   for (j=1;j<=n;j++) {    read end of parameter file: agemin, agemax, bage, fage, estepm
     pcom[j]=p[j];        begin-prev-date,...
     xicom[j]=xi[j];    open gnuplot file
   }    open html file
   ax=0.0;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   xx=1.0;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      freexexit2 possible for memory heap.
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    h Pij x                         | pij_nom  ficrestpij
 #endif     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   for (j=1;j<=n;j++) {         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
     xi[j] *= xmin;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
     p[j] += xi[j];  
   }         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   free_vector(xicom,1,n);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   free_vector(pcom,1,n);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
 }     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
      Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    forecasting if prevfcast==1 prevforecast call prevalence()
             double (*func)(double []))    health expectancies
 {    Variance-covariance of DFLE
   void linmin(double p[], double xi[], int n, double *fret,    prevalence()
               double (*func)(double []));     movingaverage()
   int i,ibig,j;    varevsij() 
   double del,t,*pt,*ptt,*xit;    if popbased==1 varevsij(,popbased)
   double fp,fptt;    total life expectancies
   double *xits;    Variance of period (stable) prevalence
   pt=vector(1,n);   end
   ptt=vector(1,n);  */
   xit=vector(1,n);  
   xits=vector(1,n);  #define POWELL /* Instead of NLOPT */
   *fret=(*func)(p);  /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  #include <math.h>
     fp=(*fret);  #include <stdio.h>
     ibig=0;  #include <stdlib.h>
     del=0.0;  #include <string.h>
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  #ifdef _WIN32
       printf(" %d %.12f",i, p[i]);  #include <io.h>
     printf("\n");  #include <windows.h>
     for (i=1;i<=n;i++) {  #include <tchar.h>
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #else
       fptt=(*fret);  #include <unistd.h>
 #ifdef DEBUG  #endif
       printf("fret=%lf \n",*fret);  
 #endif  #include <limits.h>
       printf("%d",i);fflush(stdout);  #include <sys/types.h>
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  #if defined(__GNUC__)
         del=fabs(fptt-(*fret));  #include <sys/utsname.h> /* Doesn't work on Windows */
         ibig=i;  #endif
       }  
 #ifdef DEBUG  #include <sys/stat.h>
       printf("%d %.12e",i,(*fret));  #include <errno.h>
       for (j=1;j<=n;j++) {  /* extern int errno; */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  /* #ifdef LINUX */
       }  /* #include <time.h> */
       for(j=1;j<=n;j++)  /* #include "timeval.h" */
         printf(" p=%.12e",p[j]);  /* #else */
       printf("\n");  /* #include <sys/time.h> */
 #endif  /* #endif */
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #include <time.h>
 #ifdef DEBUG  
       int k[2],l;  #ifdef GSL
       k[0]=1;  #include <gsl/gsl_errno.h>
       k[1]=-1;  #include <gsl/gsl_multimin.h>
       printf("Max: %.12e",(*func)(p));  #endif
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  
       printf("\n");  #ifdef NLOPT
       for(l=0;l<=1;l++) {  #include <nlopt.h>
         for (j=1;j<=n;j++) {  typedef struct {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double (* function)(double [] );
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  } myfunc_data ;
         }  #endif
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  /* #include <libintl.h> */
 #endif  /* #define _(String) gettext (String) */
   
   #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  #define GNUPLOTPROGRAM "gnuplot"
       free_vector(ptt,1,n);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       free_vector(pt,1,n);  #define FILENAMELENGTH 132
       return;  
     }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
       xit[j]=p[j]-pt[j];  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
       pt[j]=p[j];  
     }  #define NINTERVMAX 8
     fptt=(*func)(ptt);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     if (fptt < fp) {  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       if (t < 0.0) {  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
         linmin(p,xit,n,fret,func);  #define MAXN 20000
         for (j=1;j<=n;j++) {  #define YEARM 12. /**< Number of months per year */
           xi[j][ibig]=xi[j][n];  #define AGESUP 130
           xi[j][n]=xit[j];  #define AGEBASE 40
         }  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #ifdef DEBUG  #ifdef _WIN32
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define DIRSEPARATOR '\\'
         for(j=1;j<=n;j++)  #define CHARSEPARATOR "\\"
           printf(" %.12e",xit[j]);  #define ODIRSEPARATOR '/'
         printf("\n");  #else
 #endif  #define DIRSEPARATOR '/'
       }  #define CHARSEPARATOR "/"
     }  #define ODIRSEPARATOR '\\'
   }  #endif
 }  
   /* $Id$ */
 /**** Prevalence limit ****************/  /* $State$ */
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
 {  char fullversion[]="$Revision$ $Date$"; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  char strstart[80];
      matrix by transitions matrix until convergence is reached */  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int i, ii,j,k;  int nvar=0, nforce=0; /* Number of variables, number of forces */
   double min, max, maxmin, maxmax,sumnew=0.;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   double **matprod2();  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   double **out, cov[NCOVMAX], **pmij();  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   double **newm;  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   double agefin, delaymax=50 ; /* Max number of years to converge */  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   int cptcovprodnoage=0; /**< Number of covariate products without age */   
   for (ii=1;ii<=nlstate+ndeath;ii++)  int cptcoveff=0; /* Total number of covariates to vary for printing results */
     for (j=1;j<=nlstate+ndeath;j++){  int cptcov=0; /* Working variable */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int npar=NPARMAX;
     }  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
    cov[1]=1.;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int popbased=0;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  int *wav; /* Number of waves for this individuual 0 is possible */
     newm=savm;  int maxwav=0; /* Maxim number of waves */
     /* Covariates have to be included here again */  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
      cov[2]=agefin;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
    int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       for (k=1; k<=cptcovn;k++) {                     to the likelihood and the sum of weights (done by funcone)*/
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int mle=1, weightopt=0;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       for (k=1; k<=cptcovage;k++)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       for (k=1; k<=cptcovprod;k++)  int countcallfunc=0;  /* Count the number of calls to func */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  double jmean=1; /* Mean space between 2 waves */
   double **matprod2(); /* test */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  double **oldm, **newm, **savm; /* Working pointers to matrices */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   /*FILE *fic ; */ /* Used in readdata only */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
     savm=oldm;  int globpr=0; /* Global variable for printing or not */
     oldm=newm;  double fretone; /* Only one call to likelihood */
     maxmax=0.;  long ipmx=0; /* Number of contributions */
     for(j=1;j<=nlstate;j++){  double sw; /* Sum of weights */
       min=1.;  char filerespow[FILENAMELENGTH];
       max=0.;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       for(i=1; i<=nlstate; i++) {  FILE *ficresilk;
         sumnew=0;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  FILE *ficresprobmorprev;
         prlim[i][j]= newm[i][j]/(1-sumnew);  FILE *fichtm, *fichtmcov; /* Html File */
         max=FMAX(max,prlim[i][j]);  FILE *ficreseij;
         min=FMIN(min,prlim[i][j]);  char filerese[FILENAMELENGTH];
       }  FILE *ficresstdeij;
       maxmin=max-min;  char fileresstde[FILENAMELENGTH];
       maxmax=FMAX(maxmax,maxmin);  FILE *ficrescveij;
     }  char filerescve[FILENAMELENGTH];
     if(maxmax < ftolpl){  FILE  *ficresvij;
       return prlim;  char fileresv[FILENAMELENGTH];
     }  FILE  *ficresvpl;
   }  char fileresvpl[FILENAMELENGTH];
 }  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 /*************** transition probabilities ***************/  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  char command[FILENAMELENGTH];
 {  int  outcmd=0;
   double s1, s2;  
   /*double t34;*/  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   int i,j,j1, nc, ii, jj;  
   char filelog[FILENAMELENGTH]; /* Log file */
     for(i=1; i<= nlstate; i++){  char filerest[FILENAMELENGTH];
     for(j=1; j<i;j++){  char fileregp[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  char popfile[FILENAMELENGTH];
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       ps[i][j]=s2;  /* struct timezone tzp; */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /* extern int gettimeofday(); */
     }  struct tm tml, *gmtime(), *localtime();
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  extern time_t time();
         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);*/  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       }  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
       ps[i][j]=s2;  struct tm tm;
     }  
   }  char strcurr[80], strfor[80];
     /*ps[3][2]=1;*/  
   char *endptr;
   for(i=1; i<= nlstate; i++){  long lval;
      s1=0;  double dval;
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  #define NR_END 1
     for(j=i+1; j<=nlstate+ndeath; j++)  #define FREE_ARG char*
       s1+=exp(ps[i][j]);  #define FTOL 1.0e-10
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  #define NRANSI 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #define ITMAX 200 
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #define TOL 2.0e-4 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  #define GOLD 1.618034 
       ps[ii][ii]=1;  #define GLIMIT 100.0 
     }  #define TINY 1.0e-20 
   }  
   static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     for(jj=1; jj<= nlstate+ndeath; jj++){    
      printf("%lf ",ps[ii][jj]);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    }  #define rint(a) floor(a+0.5)
     printf("\n ");  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
     }  #define mytinydouble 1.0e-16
     printf("\n ");printf("%lf ",cov[2]);*/  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
 /*  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /* static double dsqrarg; */
   goto end;*/  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
     return ps;  static double sqrarg;
 }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 /**************** Product of 2 matrices ******************/  int agegomp= AGEGOMP;
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  int imx; 
 {  int stepm=1;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /* Stepm, step in month: minimum step interpolation*/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  int estepm;
      before: only the contents of out is modified. The function returns  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
      a pointer to pointers identical to out */  
   long i, j, k;  int m,nb;
   for(i=nrl; i<= nrh; i++)  long *num;
     for(k=ncolol; k<=ncoloh; k++)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         out[i][k] +=in[i][j]*b[j][k];  double **pmmij, ***probs;
   double *ageexmed,*agecens;
   return out;  double dateintmean=0;
 }  
   double *weight;
   int **s; /* Status */
 /************* Higher Matrix Product ***************/  double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )                    * covar=matrix(0,NCOVMAX,1,n); 
 {                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  double  idx; 
      duration (i.e. until  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  int *Ndum; /** Freq of modality (tricode */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  int **codtab; /**< codtab=imatrix(1,100,1,10); */
      (typically every 2 years instead of every month which is too big).  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
      Model is determined by parameters x and covariates have to be  double *lsurv, *lpop, *tpop;
      included manually here.  
   double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
      */  double ftolhess; /**< Tolerance for computing hessian */
   
   int i, j, d, h, k;  /**************** split *************************/
   double **out, cov[NCOVMAX];  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   double **newm;  {
     /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   /* Hstepm could be zero and should return the unit matrix */       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   for (i=1;i<=nlstate+ndeath;i++)    */ 
     for (j=1;j<=nlstate+ndeath;j++){    char  *ss;                            /* pointer */
       oldm[i][j]=(i==j ? 1.0 : 0.0);    int   l1, l2;                         /* length counters */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }    l1 = strlen(path );                   /* length of path */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(h=1; h <=nhstepm; h++){    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     for(d=1; d <=hstepm; d++){    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       newm=savm;      strcpy( name, path );               /* we got the fullname name because no directory */
       /* Covariates have to be included here again */      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       cov[1]=1.;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      /* get current working directory */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      /*    extern  char* getcwd ( char *buf , int len);*/
       for (k=1; k<=cptcovage;k++)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        return( GLOCK_ERROR_GETCWD );
       for (k=1; k<=cptcovprod;k++)      }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      ss++;                               /* after this, the filename */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      l2 = strlen( ss );                  /* length of filename */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      strcpy( name, ss );         /* save file name */
       savm=oldm;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       oldm=newm;      dirc[l1-l2] = 0;                    /* add zero */
     }      printf(" DIRC2 = %s \n",dirc);
     for(i=1; i<=nlstate+ndeath; i++)    }
       for(j=1;j<=nlstate+ndeath;j++) {    /* We add a separator at the end of dirc if not exists */
         po[i][j][h]=newm[i][j];    l1 = strlen( dirc );                  /* length of directory */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    if( dirc[l1-1] != DIRSEPARATOR ){
          */      dirc[l1] =  DIRSEPARATOR;
       }      dirc[l1+1] = 0; 
   } /* end h */      printf(" DIRC3 = %s \n",dirc);
   return po;    }
 }    ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
       ss++;
 /*************** log-likelihood *************/      strcpy(ext,ss);                     /* save extension */
 double func( double *x)      l1= strlen( name);
 {      l2= strlen(ss)+1;
   int i, ii, j, k, mi, d, kk;      strncpy( finame, name, l1-l2);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      finame[l1-l2]= 0;
   double **out;    }
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */    return( 0 );                          /* we're done */
   long ipmx;  }
   /*extern weight */  
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  /******************************************/
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  void replace_back_to_slash(char *s, char*t)
   */  {
   cov[1]=1.;    int i;
     int lg=0;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    i=0;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    lg=strlen(t);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for(i=0; i<= lg; i++) {
     for(mi=1; mi<= wav[i]-1; mi++){      (s[i] = t[i]);
       for (ii=1;ii<=nlstate+ndeath;ii++)      if (t[i]== '\\') s[i]='/';
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    }
       for(d=0; d<dh[mi][i]; d++){  }
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  char *trimbb(char *out, char *in)
         for (kk=1; kk<=cptcovage;kk++) {  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    char *s;
         }    s=out;
            while (*in != '\0'){
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        in++;
         savm=oldm;      }
         oldm=newm;      *out++ = *in++;
            }
            *out='\0';
       } /* end mult */    return s;
        }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  char *cutl(char *blocc, char *alocc, char *in, char occ)
       ipmx +=1;  {
       sw += weight[i];    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     } /* end of wave */       gives blocc="abcdef2ghi" and alocc="j".
   } /* end of individual */       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    char *s, *t;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    t=in;s=in;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    while ((*in != occ) && (*in != '\0')){
   return -l;      *alocc++ = *in++;
 }    }
     if( *in == occ){
       *(alocc)='\0';
 /*********** Maximum Likelihood Estimation ***************/      s=++in;
     }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))   
 {    if (s == t) {/* occ not found */
   int i,j, iter;      *(alocc-(in-s))='\0';
   double **xi,*delti;      in=s;
   double fret;    }
   xi=matrix(1,npar,1,npar);    while ( *in != '\0'){
   for (i=1;i<=npar;i++)      *blocc++ = *in++;
     for (j=1;j<=npar;j++)    }
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");    *blocc='\0';
   powell(p,xi,npar,ftol,&iter,&fret,func);    return t;
   }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  char *cutv(char *blocc, char *alocc, char *in, char occ)
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  {
     /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
 }       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
 /**** Computes Hessian and covariance matrix ***/       If occ is not found blocc is null and alocc is equal to in. Returns alocc
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    */
 {    char *s, *t;
   double  **a,**y,*x,pd;    t=in;s=in;
   double **hess;    while (*in != '\0'){
   int i, j,jk;      while( *in == occ){
   int *indx;        *blocc++ = *in++;
         s=in;
   double hessii(double p[], double delta, int theta, double delti[]);      }
   double hessij(double p[], double delti[], int i, int j);      *blocc++ = *in++;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    }
   void ludcmp(double **a, int npar, int *indx, double *d) ;    if (s == t) /* occ not found */
       *(blocc-(in-s))='\0';
   hess=matrix(1,npar,1,npar);    else
       *(blocc-(in-s)-1)='\0';
   printf("\nCalculation of the hessian matrix. Wait...\n");    in=s;
   for (i=1;i<=npar;i++){    while ( *in != '\0'){
     printf("%d",i);fflush(stdout);      *alocc++ = *in++;
     hess[i][i]=hessii(p,ftolhess,i,delti);    }
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/    *alocc='\0';
   }    return s;
    }
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {  int nbocc(char *s, char occ)
       if (j>i) {  {
         printf(".%d%d",i,j);fflush(stdout);    int i,j=0;
         hess[i][j]=hessij(p,delti,i,j);    int lg=20;
         hess[j][i]=hess[i][j];        i=0;
         /*printf(" %lf ",hess[i][j]);*/    lg=strlen(s);
       }    for(i=0; i<= lg; i++) {
     }    if  (s[i] == occ ) j++;
   }    }
   printf("\n");    return j;
   }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
    /* void cutv(char *u,char *v, char*t, char occ) */
   a=matrix(1,npar,1,npar);  /* { */
   y=matrix(1,npar,1,npar);  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   x=vector(1,npar);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   indx=ivector(1,npar);  /*      gives u="abcdef2ghi" and v="j" *\/ */
   for (i=1;i<=npar;i++)  /*   int i,lg,j,p=0; */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*   i=0; */
   ludcmp(a,npar,indx,&pd);  /*   lg=strlen(t); */
   /*   for(j=0; j<=lg-1; j++) { */
   for (j=1;j<=npar;j++) {  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     for (i=1;i<=npar;i++) x[i]=0;  /*   } */
     x[j]=1;  
     lubksb(a,npar,indx,x);  /*   for(j=0; j<p; j++) { */
     for (i=1;i<=npar;i++){  /*     (u[j] = t[j]); */
       matcov[i][j]=x[i];  /*   } */
     }  /*      u[p]='\0'; */
   }  
   /*    for(j=0; j<= lg; j++) { */
   printf("\n#Hessian matrix#\n");  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   for (i=1;i<=npar;i++) {  /*   } */
     for (j=1;j<=npar;j++) {  /* } */
       printf("%.3e ",hess[i][j]);  
     }  #ifdef _WIN32
     printf("\n");  char * strsep(char **pp, const char *delim)
   }  {
     char *p, *q;
   /* Recompute Inverse */           
   for (i=1;i<=npar;i++)    if ((p = *pp) == NULL)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      return 0;
   ludcmp(a,npar,indx,&pd);    if ((q = strpbrk (p, delim)) != NULL)
     {
   /*  printf("\n#Hessian matrix recomputed#\n");      *pp = q + 1;
       *q = '\0';
   for (j=1;j<=npar;j++) {    }
     for (i=1;i<=npar;i++) x[i]=0;    else
     x[j]=1;      *pp = 0;
     lubksb(a,npar,indx,x);    return p;
     for (i=1;i<=npar;i++){  }
       y[i][j]=x[i];  #endif
       printf("%.3e ",y[i][j]);  
     }  /********************** nrerror ********************/
     printf("\n");  
   }  void nrerror(char error_text[])
   */  {
     fprintf(stderr,"ERREUR ...\n");
   free_matrix(a,1,npar,1,npar);    fprintf(stderr,"%s\n",error_text);
   free_matrix(y,1,npar,1,npar);    exit(EXIT_FAILURE);
   free_vector(x,1,npar);  }
   free_ivector(indx,1,npar);  /*********************** vector *******************/
   free_matrix(hess,1,npar,1,npar);  double *vector(int nl, int nh)
   {
     double *v;
 }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 /*************** hessian matrix ****************/    return v-nl+NR_END;
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /************************ free vector ******************/
   int l=1, lmax=20;  void free_vector(double*v, int nl, int nh)
   double k1,k2;  {
   double p2[NPARMAX+1];    free((FREE_ARG)(v+nl-NR_END));
   double res;  }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;  /************************ivector *******************************/
   int k=0,kmax=10;  int *ivector(long nl,long nh)
   double l1;  {
     int *v;
   fx=func(x);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   for (i=1;i<=npar;i++) p2[i]=x[i];    if (!v) nrerror("allocation failure in ivector");
   for(l=0 ; l <=lmax; l++){    return v-nl+NR_END;
     l1=pow(10,l);  }
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  /******************free ivector **************************/
       delt = delta*(l1*k);  void free_ivector(int *v, long nl, long nh)
       p2[theta]=x[theta] +delt;  {
       k1=func(p2)-fx;    free((FREE_ARG)(v+nl-NR_END));
       p2[theta]=x[theta]-delt;  }
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */  /************************lvector *******************************/
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  long *lvector(long nl,long nh)
        {
 #ifdef DEBUG    long *v;
       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);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 #endif    if (!v) nrerror("allocation failure in ivector");
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    return v-nl+NR_END;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  }
         k=kmax;  
       }  /******************free lvector **************************/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  void free_lvector(long *v, long nl, long nh)
         k=kmax; l=lmax*10.;  {
       }    free((FREE_ARG)(v+nl-NR_END));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  }
         delts=delt;  
       }  /******************* imatrix *******************************/
     }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   delti[theta]=delts;  { 
   return res;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
      int **m; 
 }    
     /* allocate pointers to rows */ 
 double hessij( double x[], double delti[], int thetai,int thetaj)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 {    if (!m) nrerror("allocation failure 1 in matrix()"); 
   int i;    m += NR_END; 
   int l=1, l1, lmax=20;    m -= nrl; 
   double k1,k2,k3,k4,res,fx;    
   double p2[NPARMAX+1];    
   int k;    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   fx=func(x);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for (k=1; k<=2; k++) {    m[nrl] += NR_END; 
     for (i=1;i<=npar;i++) p2[i]=x[i];    m[nrl] -= ncl; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     k1=func(p2)-fx;    
      /* return pointer to array of pointers to rows */ 
     p2[thetai]=x[thetai]+delti[thetai]/k;    return m; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  } 
     k2=func(p2)-fx;  
    /****************** free_imatrix *************************/
     p2[thetai]=x[thetai]-delti[thetai]/k;  void free_imatrix(m,nrl,nrh,ncl,nch)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        int **m;
     k3=func(p2)-fx;        long nch,ncl,nrh,nrl; 
         /* free an int matrix allocated by imatrix() */ 
     p2[thetai]=x[thetai]-delti[thetai]/k;  { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     k4=func(p2)-fx;    free((FREE_ARG) (m+nrl-NR_END)); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  } 
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  /******************* matrix *******************************/
 #endif  double **matrix(long nrl, long nrh, long ncl, long nch)
   }  {
   return res;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /************** Inverse of matrix **************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void ludcmp(double **a, int n, int *indx, double *d)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   int i,imax,j,k;    m -= nrl;
   double big,dum,sum,temp;  
   double *vv;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   vv=vector(1,n);    m[nrl] += NR_END;
   *d=1.0;    m[nrl] -= ncl;
   for (i=1;i<=n;i++) {  
     big=0.0;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for (j=1;j<=n;j++)    return m;
       if ((temp=fabs(a[i][j])) > big) big=temp;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     vv[i]=1.0/big;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   }     */
   for (j=1;j<=n;j++) {  }
     for (i=1;i<j;i++) {  
       sum=a[i][j];  /*************************free matrix ************************/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       a[i][j]=sum;  {
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     big=0.0;    free((FREE_ARG)(m+nrl-NR_END));
     for (i=j;i<=n;i++) {  }
       sum=a[i][j];  
       for (k=1;k<j;k++)  /******************* ma3x *******************************/
         sum -= a[i][k]*a[k][j];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       a[i][j]=sum;  {
       if ( (dum=vv[i]*fabs(sum)) >= big) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         big=dum;    double ***m;
         imax=i;  
       }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     if (j != imax) {    m += NR_END;
       for (k=1;k<=n;k++) {    m -= nrl;
         dum=a[imax][k];  
         a[imax][k]=a[j][k];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         a[j][k]=dum;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       }    m[nrl] += NR_END;
       *d = -(*d);    m[nrl] -= ncl;
       vv[imax]=vv[j];  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (j != n) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       dum=1.0/(a[j][j]);    m[nrl][ncl] += NR_END;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    m[nrl][ncl] -= nll;
     }    for (j=ncl+1; j<=nch; j++) 
   }      m[nrl][j]=m[nrl][j-1]+nlay;
   free_vector(vv,1,n);  /* Doesn't work */    
 ;    for (i=nrl+1; i<=nrh; i++) {
 }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
 void lubksb(double **a, int n, int *indx, double b[])        m[i][j]=m[i][j-1]+nlay;
 {    }
   int i,ii=0,ip,j;    return m; 
   double sum;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
               &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   for (i=1;i<=n;i++) {    */
     ip=indx[i];  }
     sum=b[ip];  
     b[ip]=b[i];  /*************************free ma3x ************************/
     if (ii)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  {
     else if (sum) ii=i;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     b[i]=sum;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   }    free((FREE_ARG)(m+nrl-NR_END));
   for (i=n;i>=1;i--) {  }
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*************** function subdirf ***********/
     b[i]=sum/a[i][i];  char *subdirf(char fileres[])
   }  {
 }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 /************ Frequencies ********************/    strcat(tmpout,"/"); /* Add to the right */
 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)    strcat(tmpout,fileres);
 {  /* Some frequencies */    return tmpout;
    }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  /*************** function subdirf2 ***********/
   double *pp;  char *subdirf2(char fileres[], char *preop)
   double pos, k2, dateintsum=0,k2cpt=0;  {
   FILE *ficresp;    
   char fileresp[FILENAMELENGTH];    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   pp=vector(1,nlstate);    strcat(tmpout,"/");
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(tmpout,preop);
   strcpy(fileresp,"p");    strcat(tmpout,fileres);
   strcat(fileresp,fileres);    return tmpout;
   if((ficresp=fopen(fileresp,"w"))==NULL) {  }
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  {
   j1=0;    
     /* Caution optionfilefiname is hidden */
   j=cptcoveff;    strcpy(tmpout,optionfilefiname);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    strcat(tmpout,"/");
     strcat(tmpout,preop);
   for(k1=1; k1<=j;k1++){    strcat(tmpout,preop2);
    for(i1=1; i1<=ncodemax[k1];i1++){    strcat(tmpout,fileres);
        j1++;    return tmpout;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  }
          scanf("%d", i);*/  
         for (i=-1; i<=nlstate+ndeath; i++)    char *asc_diff_time(long time_sec, char ascdiff[])
          for (jk=-1; jk<=nlstate+ndeath; jk++)    {
            for(m=agemin; m <= agemax+3; m++)    long sec_left, days, hours, minutes;
              freq[i][jk][m]=0;    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
         dateintsum=0;    hours = (sec_left) / (60*60) ;
         k2cpt=0;    sec_left = (sec_left) %(60*60);
        for (i=1; i<=imx; i++) {    minutes = (sec_left) /60;
          bool=1;    sec_left = (sec_left) % (60);
          if  (cptcovn>0) {    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
            for (z1=1; z1<=cptcoveff; z1++)    return ascdiff;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  }
                bool=0;  
          }  /***************** f1dim *************************/
          if (bool==1) {  extern int ncom; 
            for(m=firstpass; m<=lastpass; m++){  extern double *pcom,*xicom;
              k2=anint[m][i]+(mint[m][i]/12.);  extern double (*nrfunc)(double []); 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {   
                if(agev[m][i]==0) agev[m][i]=agemax+1;  double f1dim(double x) 
                if(agev[m][i]==1) agev[m][i]=agemax+2;  { 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    int j; 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double f;
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    double *xt; 
                  dateintsum=dateintsum+k2;   
                  k2cpt++;    xt=vector(1,ncom); 
                }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
              }    free_vector(xt,1,ncom); 
            }    return f; 
          }  } 
        }  
         if  (cptcovn>0) {  /*****************brent *************************/
          fprintf(ficresp, "\n#********** Variable ");  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  { 
        fprintf(ficresp, "**********\n#");    int iter; 
         }    double a,b,d,etemp;
        for(i=1; i<=nlstate;i++)    double fu=0,fv,fw,fx;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double ftemp=0.;
        fprintf(ficresp, "\n");    double p,q,r,tol1,tol2,u,v,w,x,xm; 
            double e=0.0; 
   for(i=(int)agemin; i <= (int)agemax+3; i++){   
     if(i==(int)agemax+3)    a=(ax < cx ? ax : cx); 
       printf("Total");    b=(ax > cx ? ax : cx); 
     else    x=w=v=bx; 
       printf("Age %d", i);    fw=fv=fx=(*f)(x); 
     for(jk=1; jk <=nlstate ; jk++){    for (iter=1;iter<=ITMAX;iter++) { 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      xm=0.5*(a+b); 
         pp[jk] += freq[jk][m][i];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for(jk=1; jk <=nlstate ; jk++){      printf(".");fflush(stdout);
       for(m=-1, pos=0; m <=0 ; m++)      fprintf(ficlog,".");fflush(ficlog);
         pos += freq[jk][m][i];  #ifdef DEBUGBRENT
       if(pp[jk]>=1.e-10)      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      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);
       else      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  #endif
     }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
      for(jk=1; jk <=nlstate ; jk++){        return fx; 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      } 
         pp[jk] += freq[jk][m][i];      ftemp=fu;
      }      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
     for(jk=1,pos=0; jk <=nlstate ; jk++)        q=(x-v)*(fx-fw); 
       pos += pp[jk];        p=(x-v)*q-(x-w)*r; 
     for(jk=1; jk <=nlstate ; jk++){        q=2.0*(q-r); 
       if(pos>=1.e-5)        if (q > 0.0) p = -p; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        q=fabs(q); 
       else        etemp=e; 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        e=d; 
       if( i <= (int) agemax){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         if(pos>=1.e-5){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        else { 
           probs[i][jk][j1]= pp[jk]/pos;          d=p/q; 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          u=x+d; 
         }          if (u-a < tol2 || b-u < tol2) 
       else            d=SIGN(tol1,xm-x); 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        } 
       }      } else { 
     }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for(jk=-1; jk <=nlstate+ndeath; jk++)      } 
       for(m=-1; m <=nlstate+ndeath; m++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      fu=(*f)(u); 
     if(i <= (int) agemax)      if (fu <= fx) { 
       fprintf(ficresp,"\n");        if (u >= x) a=x; else b=x; 
     printf("\n");        SHFT(v,w,x,u) 
     }        SHFT(fv,fw,fx,fu) 
     }      } else { 
  }        if (u < x) a=u; else b=u; 
   dateintmean=dateintsum/k2cpt;        if (fu <= fw || w == x) { 
            v=w; 
   fclose(ficresp);          w=u; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          fv=fw; 
   free_vector(pp,1,nlstate);          fw=fu; 
         } else if (fu <= fv || v == x || v == w) { 
   /* End of Freq */          v=u; 
 }          fv=fu; 
         } 
 /************ Prevalence ********************/      } 
 void prevalence(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 calagedate)    } 
 {  /* Some frequencies */    nrerror("Too many iterations in brent"); 
      *xmin=x; 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    return fx; 
   double ***freq; /* Frequencies */  } 
   double *pp;  
   double pos, k2;  /****************** mnbrak ***********************/
   
   pp=vector(1,nlstate);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);              double (*func)(double)) 
    { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  the downhill direction (defined by the function as evaluated at the initial points) and returns
   j1=0;  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.
   j=cptcoveff;     */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double ulim,u,r,q, dum;
      double fu; 
  for(k1=1; k1<=j;k1++){   
     for(i1=1; i1<=ncodemax[k1];i1++){    *fa=(*func)(*ax); 
       j1++;    *fb=(*func)(*bx); 
      if (*fb > *fa) { 
       for (i=-1; i<=nlstate+ndeath; i++)        SHFT(dum,*ax,*bx,dum) 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        SHFT(dum,*fb,*fa,dum) 
           for(m=agemin; m <= agemax+3; m++)    } 
             freq[i][jk][m]=0;    *cx=(*bx)+GOLD*(*bx-*ax); 
          *fc=(*func)(*cx); 
       for (i=1; i<=imx; i++) {  #ifdef DEBUG
         bool=1;    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
         if  (cptcovn>0) {    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
           for (z1=1; z1<=cptcoveff; z1++)  #endif
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
               bool=0;      r=(*bx-*ax)*(*fb-*fc); 
         }      q=(*bx-*cx)*(*fb-*fa); 
         if (bool==1) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
           for(m=firstpass; m<=lastpass; m++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
             k2=anint[m][i]+(mint[m][i]/12.);      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
               if(agev[m][i]==0) agev[m][i]=agemax+1;        fu=(*func)(u); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;  #ifdef DEBUG
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        /* f(x)=A(x-u)**2+f(u) */
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];          double A, fparabu; 
             }        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
           }        fparabu= *fa - A*(*ax-u)*(*ax-u);
         }        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
       }        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
              /* And thus,it can be that fu > *fc even if fparabu < *fc */
         for(i=(int)agemin; i <= (int)agemax+3; i++){        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
           for(jk=1; jk <=nlstate ; jk++){          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
               pp[jk] += freq[jk][m][i];  #endif 
           }  #ifdef MNBRAKORI
           for(jk=1; jk <=nlstate ; jk++){  #else
             for(m=-1, pos=0; m <=0 ; m++)        if (fu > *fc) {
             pos += freq[jk][m][i];  #ifdef DEBUG
         }        printf("mnbrak4  fu > fc \n");
                fprintf(ficlog, "mnbrak4 fu > fc\n");
          for(jk=1; jk <=nlstate ; jk++){  #endif
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          /* 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 *\/  */
              pp[jk] += freq[jk][m][i];          /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
          }          dum=u; /* Shifting c and u */
                    u = *cx;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          *cx = dum;
           dum = fu;
          for(jk=1; jk <=nlstate ; jk++){                    fu = *fc;
            if( i <= (int) agemax){          *fc =dum;
              if(pos>=1.e-5){        } else { /* end */
                probs[i][jk][j1]= pp[jk]/pos;  #ifdef DEBUG
              }        printf("mnbrak3  fu < fc \n");
            }        fprintf(ficlog, "mnbrak3 fu < fc\n");
          }  #endif
                    dum=u; /* Shifting c and u */
         }          u = *cx;
     }          *cx = dum;
   }          dum = fu;
            fu = *fc;
            *fc =dum;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        }
   free_vector(pp,1,nlstate);  #endif
        } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
 }  /* End of Freq */  #ifdef DEBUG
         printf("mnbrak2  u after c but before ulim\n");
 /************* Waves Concatenation ***************/        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
   #endif
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        fu=(*func)(u); 
 {        if (fu < *fc) { 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  #ifdef DEBUG
      Death is a valid wave (if date is known).        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  #endif
      and mw[mi+1][i]. dh depends on stepm.          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
      */          SHFT(*fb,*fc,fu,(*func)(u)) 
         } 
   int i, mi, m;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  #ifdef DEBUG
      double sum=0., jmean=0.;*/        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
         fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
   int j, k=0,jk, ju, jl;  #endif
   double sum=0.;        u=ulim; 
   jmin=1e+5;        fu=(*func)(u); 
   jmax=-1;      } else { /* u could be left to b (if r > q parabola has a maximum) */
   jmean=0.;  #ifdef DEBUG
   for(i=1; i<=imx; i++){        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
     mi=0;        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
     m=firstpass;  #endif
     while(s[m][i] <= nlstate){        u=(*cx)+GOLD*(*cx-*bx); 
       if(s[m][i]>=1)        fu=(*func)(u); 
         mw[++mi][i]=m;      } /* end tests */
       if(m >=lastpass)      SHFT(*ax,*bx,*cx,u) 
         break;      SHFT(*fa,*fb,*fc,fu) 
       else  #ifdef DEBUG
         m++;        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);
     }/* end while */        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);
     if (s[m][i] > nlstate){  #endif
       mi++;     /* Death is another wave */    } /* 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(mi==0)  never been interviewed correctly before death */  } 
          /* Only death is a correct wave */  
       mw[mi][i]=m;  /*************** 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 ,
     wav[i]=mi;  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
     if(mi==0)  the value of func at the returned location p . This is actually all accomplished by calling the
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  routines mnbrak and brent .*/
   }  int ncom; 
   double *pcom,*xicom;
   for(i=1; i<=imx; i++){  double (*nrfunc)(double []); 
     for(mi=1; mi<wav[i];mi++){   
       if (stepm <=0)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         dh[mi][i]=1;  { 
       else{    double brent(double ax, double bx, double cx, 
         if (s[mw[mi+1][i]][i] > nlstate) {                 double (*f)(double), double tol, double *xmin); 
           if (agedc[i] < 2*AGESUP) {    double f1dim(double x); 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
           if(j==0) j=1;  /* Survives at least one month after exam */                double *fc, double (*func)(double)); 
           k=k+1;    int j; 
           if (j >= jmax) jmax=j;    double xx,xmin,bx,ax; 
           if (j <= jmin) jmin=j;    double fx,fb,fa;
           sum=sum+j;   
           /* if (j<10) printf("j=%d num=%d ",j,i); */    ncom=n; 
           }    pcom=vector(1,n); 
         }    xicom=vector(1,n); 
         else{    nrfunc=func; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    for (j=1;j<=n;j++) { 
           k=k+1;      pcom[j]=p[j]; 
           if (j >= jmax) jmax=j;      xicom[j]=xi[j]; 
           else if (j <= jmin)jmin=j;    } 
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    ax=0.0; 
           sum=sum+j;    xx=1.0; 
         }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
         jk= j/stepm;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
         jl= j -jk*stepm;  #ifdef DEBUG
         ju= j -(jk+1)*stepm;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         if(jl <= -ju)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           dh[mi][i]=jk;  #endif
         else    for (j=1;j<=n;j++) { 
           dh[mi][i]=jk+1;      xi[j] *= xmin; 
         if(dh[mi][i]==0)      p[j] += xi[j]; 
           dh[mi][i]=1; /* At least one step */    } 
       }    free_vector(xicom,1,n); 
     }    free_vector(pcom,1,n); 
   }  } 
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  
  }  /*************** powell ************************/
 /*********** Tricode ****************************/  /*
 void tricode(int *Tvar, int **nbcode, int imx)  Minimization of a function func of n variables. Input consists of an initial starting point
 {  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   int Ndum[20],ij=1, k, j, i;  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   int cptcode=0;  such that failure to decrease by more than this amount on one iteration signals doneness. On
   cptcoveff=0;  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
    function value at p , and iter is the number of iterations taken. The routine linmin is used.
   for (k=0; k<19; k++) Ndum[k]=0;   */
   for (k=1; k<=7; k++) ncodemax[k]=0;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  { 
     for (i=1; i<=imx; i++) {    void linmin(double p[], double xi[], int n, double *fret, 
       ij=(int)(covar[Tvar[j]][i]);                double (*func)(double [])); 
       Ndum[ij]++;    int i,ibig,j; 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    double del,t,*pt,*ptt,*xit;
       if (ij > cptcode) cptcode=ij;    double directest;
     }    double fp,fptt;
     double *xits;
     for (i=0; i<=cptcode; i++) {    int niterf, itmp;
       if(Ndum[i]!=0) ncodemax[j]++;  
     }    pt=vector(1,n); 
     ij=1;    ptt=vector(1,n); 
     xit=vector(1,n); 
     xits=vector(1,n); 
     for (i=1; i<=ncodemax[j]; i++) {    *fret=(*func)(p); 
       for (k=0; k<=19; k++) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
         if (Ndum[k] != 0) {      rcurr_time = time(NULL);  
           nbcode[Tvar[j]][ij]=k;    for (*iter=1;;++(*iter)) { 
           ij++;      fp=(*fret); 
         }      ibig=0; 
         if (ij > ncodemax[j]) break;      del=0.0; 
       }        rlast_time=rcurr_time;
     }      /* (void) gettimeofday(&curr_time,&tzp); */
   }        rcurr_time = time(NULL);  
       curr_time = *localtime(&rcurr_time);
  for (k=0; k<19; k++) Ndum[k]=0;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
  for (i=1; i<=ncovmodel-2; i++) {  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
       ij=Tvar[i];     for (i=1;i<=n;i++) {
       Ndum[ij]++;        printf(" %d %.12f",i, p[i]);
     }        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
  ij=1;      }
  for (i=1; i<=10; i++) {      printf("\n");
    if((Ndum[i]!=0) && (i<=ncov)){      fprintf(ficlog,"\n");
      Tvaraff[ij]=i;      fprintf(ficrespow,"\n");fflush(ficrespow);
      ij++;      if(*iter <=3){
    }        tml = *localtime(&rcurr_time);
  }        strcpy(strcurr,asctime(&tml));
          rforecast_time=rcurr_time; 
     cptcoveff=ij-1;        itmp = strlen(strcurr);
 }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
 /*********** Health Expectancies ****************/        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);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        for(niterf=10;niterf<=30;niterf+=10){
 {          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
   /* Health expectancies */          forecast_time = *localtime(&rforecast_time);
   int i, j, nhstepm, hstepm, h;          strcpy(strfor,asctime(&forecast_time));
   double age, agelim,hf;          itmp = strlen(strfor);
   double ***p3mat;          if(strfor[itmp-1]=='\n')
            strfor[itmp-1]='\0';
   fprintf(ficreseij,"# Health expectancies\n");          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(ficreseij,"# Age");          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
   for(i=1; i<=nlstate;i++)        }
     for(j=1; j<=nlstate;j++)      }
       fprintf(ficreseij," %1d-%1d",i,j);      for (i=1;i<=n;i++) { 
   fprintf(ficreseij,"\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   hstepm=1*YEARM; /*  Every j years of age (in month) */  #ifdef DEBUG
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
             fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   agelim=AGESUP;  #endif
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        printf("%d",i);fflush(stdout);
     /* nhstepm age range expressed in number of stepm */        fprintf(ficlog,"%d",i);fflush(ficlog);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
     /* Typically if 20 years = 20*12/6=40 stepm */        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
     if (stepm >= YEARM) hstepm=1;                                         because that direction will be replaced unless the gain del is small
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */                                        in comparison with the 'probable' gain, mu^2, with the last average direction.
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                        Unless the n directions are conjugate some gain in the determinant may be obtained
     /* Computed by stepm unit matrices, product of hstepm matrices, stored                                        with the new direction.
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                                        */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            del=fabs(fptt-(*fret)); 
           ibig=i; 
         } 
     for(i=1; i<=nlstate;i++)  #ifdef DEBUG
       for(j=1; j<=nlstate;j++)        printf("%d %.12e",i,(*fret));
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        fprintf(ficlog,"%d %.12e",i,(*fret));
           eij[i][j][(int)age] +=p3mat[i][j][h];        for (j=1;j<=n;j++) {
         }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
              printf(" x(%d)=%.12e",j,xit[j]);
     hf=1;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     if (stepm >= YEARM) hf=stepm/YEARM;        }
     fprintf(ficreseij,"%.0f",age );        for(j=1;j<=n;j++) {
     for(i=1; i<=nlstate;i++)          printf(" p(%d)=%.12e",j,p[j]);
       for(j=1; j<=nlstate;j++){          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        }
       }        printf("\n");
     fprintf(ficreseij,"\n");        fprintf(ficlog,"\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #endif
   }      } /* end i */
 }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
   #ifdef DEBUG
 /************ Variance ******************/        int k[2],l;
 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)        k[0]=1;
 {        k[1]=-1;
   /* Variance of health expectancies */        printf("Max: %.12e",(*func)(p));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double **newm;        for (j=1;j<=n;j++) {
   double **dnewm,**doldm;          printf(" %.12e",p[j]);
   int i, j, nhstepm, hstepm, h;          fprintf(ficlog," %.12e",p[j]);
   int k, cptcode;        }
   double *xp;        printf("\n");
   double **gp, **gm;        fprintf(ficlog,"\n");
   double ***gradg, ***trgradg;        for(l=0;l<=1;l++) {
   double ***p3mat;          for (j=1;j<=n;j++) {
   double age,agelim;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   int theta;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
    fprintf(ficresvij,"# Covariances of life expectancies\n");          }
   fprintf(ficresvij,"# Age");          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for(i=1; i<=nlstate;i++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(j=1; j<=nlstate;j++)        }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  #endif
   fprintf(ficresvij,"\n");  
   
   xp=vector(1,npar);        free_vector(xit,1,n); 
   dnewm=matrix(1,nlstate,1,npar);        free_vector(xits,1,n); 
   doldm=matrix(1,nlstate,1,nlstate);        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
   hstepm=1*YEARM; /* Every year of age */        return; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      } 
   agelim = AGESUP;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        ptt[j]=2.0*p[j]-pt[j]; 
     if (stepm >= YEARM) hstepm=1;        xit[j]=p[j]-pt[j]; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        pt[j]=p[j]; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      fptt=(*func)(ptt); /* f_3 */
     gp=matrix(0,nhstepm,1,nlstate);      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
     gm=matrix(0,nhstepm,1,nlstate);        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
         /* From x1 (P0) distance of x2 is at h and x3 is 2h */
     for(theta=1; theta <=npar; theta++){        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       for(i=1; i<=npar; i++){ /* Computes gradient */        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
       }        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  #ifdef NRCORIGINAL
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
       if (popbased==1) {  #else
         for(i=1; i<=nlstate;i++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
           prlim[i][i]=probs[(int)age][i][ij];        t= t- del*SQR(fp-fptt);
       }  #endif
              directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
       for(j=1; j<= nlstate; j++){  #ifdef DEBUG
         for(h=0; h<=nhstepm; h++){        printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
         }               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
       }        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                   (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
       for(i=1; i<=npar; i++) /* Computes gradient */        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);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        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);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #endif
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  #ifdef POWELLORIGINAL
         if (t < 0.0) { /* Then we use it for new direction */
       if (popbased==1) {  #else
         for(i=1; i<=nlstate;i++)        if (directest*t < 0.0) { /* Contradiction between both tests */
           prlim[i][i]=probs[(int)age][i][ij];        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);
       }        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);
       for(j=1; j<= nlstate; j++){        fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         for(h=0; h<=nhstepm; h++){      } 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        if (directest < 0.0) { /* Then we use it for new direction */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  #endif
         }          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
       }          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
       for(j=1; j<= nlstate; j++)            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
         for(h=0; h<=nhstepm; h++){          }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          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);
     } /* End theta */  
   #ifdef DEBUG
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(h=0; h<=nhstepm; h++)          for(j=1;j<=n;j++){
       for(j=1; j<=nlstate;j++)            printf(" %.12e",xit[j]);
         for(theta=1; theta <=npar; theta++)            fprintf(ficlog," %.12e",xit[j]);
           trgradg[h][j][theta]=gradg[h][theta][j];          }
           printf("\n");
     for(i=1;i<=nlstate;i++)          fprintf(ficlog,"\n");
       for(j=1;j<=nlstate;j++)  #endif
         vareij[i][j][(int)age] =0.;        } /* end of t negative */
     for(h=0;h<=nhstepm;h++){      } /* end if (fptt < fp)  */
       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++)  /**** Prevalence limit (stable or period prevalence)  ****************/
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       }  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     h=1;       matrix by transitions matrix until convergence is reached */
     if (stepm >= YEARM) h=stepm/YEARM;    
     fprintf(ficresvij,"%.0f ",age );    int i, ii,j,k;
     for(i=1; i<=nlstate;i++)    double min, max, maxmin, maxmax,sumnew=0.;
       for(j=1; j<=nlstate;j++){    /* double **matprod2(); */ /* test */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    double **out, cov[NCOVMAX+1], **pmij();
       }    double **newm;
     fprintf(ficresvij,"\n");    double agefin, delaymax=50 ; /* Max number of years to converge */
     free_matrix(gp,0,nhstepm,1,nlstate);    
     free_matrix(gm,0,nhstepm,1,nlstate);    for (ii=1;ii<=nlstate+ndeath;ii++)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      for (j=1;j<=nlstate+ndeath;j++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
   } /* End age */    
      cov[1]=1.;
   free_vector(xp,1,npar);    
   free_matrix(doldm,1,nlstate,1,npar);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   free_matrix(dnewm,1,nlstate,1,nlstate);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
 }      /* Covariates have to be included here again */
       cov[2]=agefin;
 /************ 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)      for (k=1; k<=cptcovn;k++) {
 {        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   /* Variance of prevalence limit */        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      }
   double **newm;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   double **dnewm,**doldm;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   int i, j, nhstepm, hstepm;      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   int k, cptcode;      
   double *xp;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double *gp, *gm;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   double **gradg, **trgradg;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double age,agelim;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   int theta;      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
          out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      
   fprintf(ficresvpl,"# Age");      savm=oldm;
   for(i=1; i<=nlstate;i++)      oldm=newm;
       fprintf(ficresvpl," %1d-%1d",i,i);      maxmax=0.;
   fprintf(ficresvpl,"\n");      for(j=1;j<=nlstate;j++){
         min=1.;
   xp=vector(1,npar);        max=0.;
   dnewm=matrix(1,nlstate,1,npar);        for(i=1; i<=nlstate; i++) {
   doldm=matrix(1,nlstate,1,nlstate);          sumnew=0;
            for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   hstepm=1*YEARM; /* Every year of age */          prlim[i][j]= newm[i][j]/(1-sumnew);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
   agelim = AGESUP;          max=FMAX(max,prlim[i][j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          min=FMIN(min,prlim[i][j]);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
     if (stepm >= YEARM) hstepm=1;        maxmin=max-min;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        maxmax=FMAX(maxmax,maxmin);
     gradg=matrix(1,npar,1,nlstate);      } /* j loop */
     gp=vector(1,nlstate);      if(maxmax < ftolpl){
     gm=vector(1,nlstate);        return prlim;
       }
     for(theta=1; theta <=npar; theta++){    } /* age loop */
       for(i=1; i<=npar; i++){ /* Computes gradient */    return prlim; /* should not reach here */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  }
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /*************** transition probabilities ***************/ 
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      {
       for(i=1; i<=npar; i++) /* Computes gradient */    /* According to parameters values stored in x and the covariate's values stored in cov,
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       computes the probability to be observed in state j being in state i by appying the
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       model to the ncovmodel covariates (including constant and age).
       for(i=1;i<=nlstate;i++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         gm[i] = prlim[i][i];       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
       for(i=1;i<=nlstate;i++)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     } /* End theta */       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
     trgradg =matrix(1,nlstate,1,npar);       Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     for(j=1; j<=nlstate;j++)    */
       for(theta=1; theta <=npar; theta++)    double s1, lnpijopii;
         trgradg[j][theta]=gradg[theta][j];    /*double t34;*/
     int i,j, nc, ii, jj;
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;      for(i=1; i<= nlstate; i++){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        for(j=1; j<i;j++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     for(i=1;i<=nlstate;i++)            /*lnpijopii += param[i][j][nc]*cov[nc];*/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     fprintf(ficresvpl,"%.0f ",age );          }
     for(i=1; i<=nlstate;i++)          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     fprintf(ficresvpl,"\n");        }
     free_vector(gp,1,nlstate);        for(j=i+1; j<=nlstate+ndeath;j++){
     free_vector(gm,1,nlstate);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     free_matrix(gradg,1,npar,1,nlstate);            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     free_matrix(trgradg,1,nlstate,1,npar);            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   } /* End age */  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
           }
   free_vector(xp,1,npar);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   free_matrix(doldm,1,nlstate,1,npar);        }
   free_matrix(dnewm,1,nlstate,1,nlstate);      }
       
 }      for(i=1; i<= nlstate; i++){
         s1=0;
 /************ Variance of one-step probabilities  ******************/        for(j=1; j<i; j++){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
 {          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   int i, j;        }
   int k=0, cptcode;        for(j=i+1; j<=nlstate+ndeath; j++){
   double **dnewm,**doldm;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   double *xp;          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   double *gp, *gm;        }
   double **gradg, **trgradg;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   double age,agelim, cov[NCOVMAX];        ps[i][i]=1./(s1+1.);
   int theta;        /* Computing other pijs */
   char fileresprob[FILENAMELENGTH];        for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
   strcpy(fileresprob,"prob");        for(j=i+1; j<=nlstate+ndeath; j++)
   strcat(fileresprob,fileres);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     printf("Problem with resultfile: %s\n", fileresprob);      } /* end i */
   }      
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
          for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
   xp=vector(1,npar);          ps[ii][ii]=1;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      }
        
   cov[1]=1;      
   for (age=bage; age<=fage; age ++){      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     cov[2]=age;      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     gradg=matrix(1,npar,1,9);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     trgradg=matrix(1,9,1,npar);      /*   } */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      /*   printf("\n "); */
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      /* } */
          /* printf("\n ");printf("%lf ",cov[2]);*/
     for(theta=1; theta <=npar; theta++){      /*
       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);        goto end;*/
            return ps;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  }
      
       k=0;  /**************** Product of 2 matrices ******************/
       for(i=1; i<= (nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
            k=k+1;  {
           gp[k]=pmmij[i][j];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       }    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
       for(i=1; i<=npar; i++)       a pointer to pointers identical to out */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int i, j, k;
        for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        out[i][k]=0.;
       k=0;        for(j=ncl; j<=nch; j++)
       for(i=1; i<=(nlstate+ndeath); i++){          out[i][k] +=in[i][j]*b[j][k];
         for(j=1; j<=(nlstate+ndeath);j++){      }
           k=k+1;    return out;
           gm[k]=pmmij[i][j];  }
         }  
       }  
        /************* Higher Matrix Product ***************/
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     }  {
     /* Computes the transition matrix starting at age 'age' over 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)       'nhstepm*hstepm*stepm' months (i.e. until
       for(theta=1; theta <=npar; theta++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       trgradg[j][theta]=gradg[theta][j];       nhstepm*hstepm matrices. 
         Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);       (typically every 2 years instead of every month which is too big 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);       for the memory).
        Model is determined by parameters x and covariates have to be 
      pmij(pmmij,cov,ncovmodel,x,nlstate);       included manually here. 
   
      k=0;       */
      for(i=1; i<=(nlstate+ndeath); i++){  
        for(j=1; j<=(nlstate+ndeath);j++){    int i, j, d, h, k;
          k=k+1;    double **out, cov[NCOVMAX+1];
          gm[k]=pmmij[i][j];    double **newm;
         }  
      }    /* Hstepm could be zero and should return the unit matrix */
          for (i=1;i<=nlstate+ndeath;i++)
      /*printf("\n%d ",(int)age);      for (j=1;j<=nlstate+ndeath;j++){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
                po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      }*/    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
   fprintf(ficresprob,"\n%d ",(int)age);        newm=savm;
         /* Covariates have to be included here again */
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        cov[1]=1.;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        for (k=1; k<=cptcovn;k++) 
   }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
 }  
  free_vector(xp,1,npar);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 fclose(ficresprob);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
  exit(0);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
 /******************* Printing html file ***********/        oldm=newm;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){      }
   int jj1, k1, i1, cpt;      for(i=1; i<=nlstate+ndeath; i++)
   FILE *fichtm;        for(j=1;j<=nlstate+ndeath;j++) {
   /*char optionfilehtm[FILENAMELENGTH];*/          po[i][j][h]=newm[i][j];
           /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   strcpy(optionfilehtm,optionfile);        }
   strcat(optionfilehtm,".htm");      /*printf("h=%d ",h);*/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    } /* end h */
     printf("Problem with %s \n",optionfilehtm), exit(0);  /*     printf("\n H=%d \n",h); */
   }    return po;
   }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
 Total number of observations=%d <br>    double fret;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    double *xt;
 <hr  size=\"2\" color=\"#EC5E5E\">    int j;
 <li>Outputs files<br><br>\n    myfunc_data *d2 = (myfunc_data *) pd;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  /* xt = (p1-1); */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    xt=vector(1,n); 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    printf("Function = %.12lf ",fret);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    printf("\n");
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>   free_vector(xt,1,n);
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    return fret;
    }
 fprintf(fichtm," <li>Graphs</li><p>");  #endif
   
  m=cptcoveff;  /*************** log-likelihood *************/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  double func( double *x)
   {
  jj1=0;    int i, ii, j, k, mi, d, kk;
  for(k1=1; k1<=m;k1++){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    for(i1=1; i1<=ncodemax[k1];i1++){    double **out;
        jj1++;    double sw; /* Sum of weights */
        if (cptcovn > 0) {    double lli; /* Individual log likelihood */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    int s1, s2;
          for (cpt=1; cpt<=cptcoveff;cpt++)    double bbh, survp;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    long ipmx;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /*extern weight */
        }    /* We are differentiating ll according to initial status */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        /*for(i=1;i<imx;i++) 
        for(cpt=1; cpt<nlstate;cpt++){      printf(" %d\n",s[4][i]);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }    ++countcallfunc;
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    cov[1]=1.;
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for(k=1; k<=nlstate; k++) ll[k]=0.;
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {    if(mle==1){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        /* 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[]
      fprintf(fichtm,"\n<br>- Total life expectancy by age and           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
 health expectancies in states (1) and (2): e%s%d.gif<br>           to be observed in j being in i according to the model.
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);         */
 fprintf(fichtm,"\n</body>");        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
    }          cov[2+k]=covar[Tvar[k]][i];
    }        }
 fclose(fichtm);        /* 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] 
            has been calculated etc */
 /******************* Gnuplot file **************/        for(mi=1; mi<= wav[i]-1; mi++){
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcpy(optionfilegnuplot,optionfilefiname);            }
   strcat(optionfilegnuplot,".plt");          for(d=0; d<dh[mi][i]; d++){
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            newm=savm;
     printf("Problem with file %s",optionfilegnuplot);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
 #ifdef windows            }
     fprintf(ficgp,"cd \"%s\" \n",pathc);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #endif                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 m=pow(2,cptcoveff);            savm=oldm;
              oldm=newm;
  /* 1eme*/          } /* end mult */
   for (cpt=1; cpt<= nlstate ; cpt ++) {        
    for (k1=1; k1<= m ; k1 ++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
 #ifdef windows           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);           * (in months) between two waves is not a multiple of stepm, we rounded to 
 #endif           * the nearest (and in case of equal distance, to the lowest) interval but now
 #ifdef unix           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 #endif           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 for (i=1; i<= nlstate ; i ++) {           * -stepm/2 to stepm/2 .
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           * For stepm=1 the results are the same as for previous versions of Imach.
   else fprintf(ficgp," \%%*lf (\%%*lf)");           * For stepm > 1 the results are less biased than in previous versions. 
 }           */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          s1=s[mw[mi][i]][i];
     for (i=1; i<= nlstate ; i ++) {          s2=s[mw[mi+1][i]][i];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          bbh=(double)bh[mi][i]/(double)stepm; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          /* bias bh is positive if real duration
 }           * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);           */
      for (i=1; i<= nlstate ; i ++) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          if( s2 > nlstate){ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            /* i.e. if s2 is a death state and if the date of death is known 
 }                 then the contribution to the likelihood is the probability to 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));               die between last step unit time and current  step unit time, 
 #ifdef unix               which is also equal to probability to die before dh 
 fprintf(ficgp,"\nset ter gif small size 400,300");               minus probability to die before dh-stepm . 
 #endif               In version up to 0.92 likelihood was computed
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          as if date of death was unknown. Death was treated as any other
    }          health state: the date of the interview describes the actual state
   }          and not the date of a change in health state. The former idea was
   /*2 eme*/          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
   for (k1=1; k1<= m ; k1 ++) {          introduced the exact date of death then we should have modified
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          the contribution of an exact death to the likelihood. This new
              contribution is smaller and very dependent of the step unit
     for (i=1; i<= nlstate+1 ; i ++) {          stepm. It is no more the probability to die between last interview
       k=2*i;          and month of death but the probability to survive from last
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          interview up to one month before death multiplied by the
       for (j=1; j<= nlstate+1 ; j ++) {          probability to die within a month. Thanks to Chris
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          Jackson for correcting this bug.  Former versions increased
   else fprintf(ficgp," \%%*lf (\%%*lf)");          mortality artificially. The bad side is that we add another loop
 }            which slows down the processing. The difference can be up to 10%
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          lower mortality.
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          /* If, at the beginning of the maximization mostly, the
       for (j=1; j<= nlstate+1 ; j ++) {             cumulative probability or probability to be dead is
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");             constant (ie = 1) over time d, the difference is equal to
         else fprintf(ficgp," \%%*lf (\%%*lf)");             0.  out[s1][3] = savm[s1][3]: probability, being at state
 }               s1 at precedent wave, to be dead a month before current
       fprintf(ficgp,"\" t\"\" w l 0,");             wave is equal to probability, being at state s1 at
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);             precedent wave, to be dead at mont of the current
       for (j=1; j<= nlstate+1 ; j ++) {             wave. Then the observed probability (that this person died)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");             is null according to current estimated parameter. In fact,
   else fprintf(ficgp," \%%*lf (\%%*lf)");             it should be very low but not zero otherwise the log go to
 }               infinity.
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          */
       else fprintf(ficgp,"\" t\"\" w l 0,");  /* #ifdef INFINITYORIGINAL */
     }  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  /* #else */
   }  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
    /*          lli=log(mytinydouble); */
   /*3eme*/  /*        else */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   for (k1=1; k1<= m ; k1 ++) {  /* #endif */
     for (cpt=1; cpt<= nlstate ; cpt ++) {              lli=log(out[s1][s2] - savm[s1][s2]);
       k=2+nlstate*(cpt-1);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          } else if  (s2==-2) {
       for (i=1; i< nlstate ; i ++) {            for (j=1,survp=0. ; j<=nlstate; j++) 
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            /*survp += out[s1][j]; */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            lli= log(survp);
     }          }
     }          
            else if  (s2==-4) { 
   /* CV preval stat */            for (j=3,survp=0. ; j<=nlstate; j++)  
     for (k1=1; k1<= m ; k1 ++) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for (cpt=1; cpt<nlstate ; cpt ++) {            lli= log(survp); 
       k=3;          } 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
           else if  (s2==-5) { 
       for (i=1; i< nlstate ; i ++)            for (j=1,survp=0. ; j<=2; j++)  
         fprintf(ficgp,"+$%d",k+i+1);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            lli= log(survp); 
                } 
       l=3+(nlstate+ndeath)*cpt;          
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          else{
       for (i=1; i< nlstate ; i ++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         l=3+(nlstate+ndeath)*cpt;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         fprintf(ficgp,"+$%d",l+i+1);          } 
       }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            /*if(lli ==000.0)*/
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          /*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];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* proba elementaires */          /* if (lli < log(mytinydouble)){ */
    for(i=1,jk=1; i <=nlstate; i++){          /*   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); */
     for(k=1; k <=(nlstate+ndeath); k++){          /*   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]); */
       if (k != i) {          /* } */
         for(j=1; j <=ncovmodel; j++){        } /* end of wave */
              } /* end of individual */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    }  else if(mle==2){
           jk++;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           fprintf(ficgp,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(jk=1; jk <=m; jk++) {            }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          for(d=0; d<=dh[mi][i]; d++){
    i=1;            newm=savm;
    for(k2=1; k2<=nlstate; k2++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      k3=i;            for (kk=1; kk<=cptcovage;kk++) {
      for(k=1; k<=(nlstate+ndeath); k++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        if (k != k2){            }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ij=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(j=3; j <=ncovmodel; j++) {            savm=oldm;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            oldm=newm;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          } /* end mult */
             ij++;        
           }          s1=s[mw[mi][i]][i];
           else          s2=s[mw[mi+1][i]][i];
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          bbh=(double)bh[mi][i]/(double)stepm; 
         }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           fprintf(ficgp,")/(1");          ipmx +=1;
                  sw += weight[i];
         for(k1=1; k1 <=nlstate; k1++){            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        } /* end of wave */
 ij=1;      } /* end of individual */
           for(j=3; j <=ncovmodel; j++){    }  else if(mle==3){  /* exponential inter-extrapolation */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             ij++;        for(mi=1; mi<= wav[i]-1; mi++){
           }          for (ii=1;ii<=nlstate+ndeath;ii++)
           else            for (j=1;j<=nlstate+ndeath;j++){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           fprintf(ficgp,")");            }
         }          for(d=0; d<dh[mi][i]; d++){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            newm=savm;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         i=i+ncovmodel;            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,
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    }            savm=oldm;
                oldm=newm;
   fclose(ficgp);          } /* end mult */
 }  /* end gnuplot */        
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 /*************** Moving average **************/          bbh=(double)bh[mi][i]/(double)stepm; 
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
   int i, cpt, cptcod;          sw += weight[i];
     for (agedeb=agemin; agedeb<=fage; agedeb++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for (i=1; i<=nlstate;i++)        } /* end of wave */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      } /* end of individual */
           mobaverage[(int)agedeb][i][cptcod]=0.;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (i=1; i<=nlstate;i++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (cpt=0;cpt<=4;cpt++){            for (j=1;j<=nlstate+ndeath;j++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            }
         }          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
 }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 /***********************************************/          
 /**************** Main Program *****************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /***********************************************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 int main(int argc, char *argv[])            oldm=newm;
 {          } /* end mult */
         
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          s1=s[mw[mi][i]][i];
   double agedeb, agefin,hf;          s2=s[mw[mi+1][i]][i];
   double agemin=1.e20, agemax=-1.e20;          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
   double fret;          }else{
   double **xi,tmp,delta;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
   double dum; /* Dummy variable */          ipmx +=1;
   double ***p3mat;          sw += weight[i];
   int *indx;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char line[MAXLINE], linepar[MAXLINE];  /*      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]); */
   char title[MAXLINE];        } /* end of wave */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      } /* end of individual */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   char filerest[FILENAMELENGTH];          for (ii=1;ii<=nlstate+ndeath;ii++)
   char fileregp[FILENAMELENGTH];            for (j=1;j<=nlstate+ndeath;j++){
   char popfile[FILENAMELENGTH];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int firstobs=1, lastobs=10;            }
   int sdeb, sfin; /* Status at beginning and end */          for(d=0; d<dh[mi][i]; d++){
   int c,  h , cpt,l;            newm=savm;
   int ju,jl, mi;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            for (kk=1; kk<=cptcovage;kk++) {
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int mobilav=0,popforecast=0;            }
   int hstepm, nhstepm;          
   int *popage;/*boolprev=0 if date and zero if wave*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   double bage, fage, age, agelim, agebase;            oldm=newm;
   double ftolpl=FTOL;          } /* end mult */
   double **prlim;        
   double *severity;          s1=s[mw[mi][i]][i];
   double ***param; /* Matrix of parameters */          s2=s[mw[mi+1][i]][i];
   double  *p;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double **matcov; /* Matrix of covariance */          ipmx +=1;
   double ***delti3; /* Scale */          sw += weight[i];
   double *delti; /* Scale */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double ***eij, ***vareij;          /*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]);*/
   double **varpl; /* Variances of prevalence limits by age */        } /* end of wave */
   double *epj, vepp;      } /* end of individual */
   double kk1, kk2;    } /* End of if */
   double *popeffectif,*popcount;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double yp,yp1,yp2;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";  }
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   /*************** log-likelihood *************/
   double funcone( double *x)
   char z[1]="c", occ;  {
 #include <sys/time.h>    /* Same as likeli but slower because of a lot of printf and if */
 #include <time.h>    int i, ii, j, k, mi, d, kk;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      double **out;
   /* long total_usecs;    double lli; /* Individual log likelihood */
   struct timeval start_time, end_time;    double llt;
      int s1, s2;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double bbh, survp;
     /*extern weight */
     /* We are differentiating ll according to initial status */
   printf("\n%s",version);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   if(argc <=1){    /*for(i=1;i<imx;i++) 
     printf("\nEnter the parameter file name: ");      printf(" %d\n",s[4][i]);
     scanf("%s",pathtot);    */
   }    cov[1]=1.;
   else{  
     strcpy(pathtot,argv[1]);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /*cygwin_split_path(pathtot,path,optionfile);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      for(mi=1; mi<= wav[i]-1; mi++){
   /* cutv(path,optionfile,pathtot,'\\');*/        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   chdir(path);          }
   replace(pathc,path);        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
 /*-------- arguments in the command line --------*/          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
   strcpy(fileres,"r");            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   strcat(fileres, optionfilefiname);          }
   strcat(fileres,".txt");    /* Other files have txt extension */          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /*---------arguments file --------*/                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
     printf("Problem with optionfile %s\n",optionfile);          savm=oldm;
     goto end;          oldm=newm;
   }        } /* end mult */
         
   strcpy(filereso,"o");        s1=s[mw[mi][i]][i];
   strcat(filereso,fileres);        s2=s[mw[mi+1][i]][i];
   if((ficparo=fopen(filereso,"w"))==NULL) {        bbh=(double)bh[mi][i]/(double)stepm; 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        /* bias is positive if real duration
   }         * is higher than the multiple of stepm and negative otherwise.
          */
   /* Reads comments: lines beginning with '#' */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   while((c=getc(ficpar))=='#' && c!= EOF){          lli=log(out[s1][s2] - savm[s1][s2]);
     ungetc(c,ficpar);        } else if  (s2==-2) {
     fgets(line, MAXLINE, ficpar);          for (j=1,survp=0. ; j<=nlstate; j++) 
     puts(line);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     fputs(line,ficparo);          lli= log(survp);
   }        }else if (mle==1){
   ungetc(c,ficpar);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          lli= (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 */
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        } else if(mle==3){  /* exponential inter-extrapolation */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);          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 */
 while((c=getc(ficpar))=='#' && c!= EOF){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     ungetc(c,ficpar);          lli=log(out[s1][s2]); /* Original formula */
     fgets(line, MAXLINE, ficpar);        } else{  /* mle=0 back to 1 */
     puts(line);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     fputs(line,ficparo);          /*lli=log(out[s1][s2]); */ /* Original formula */
   }        } /* End of if */
   ungetc(c,ficpar);        ipmx +=1;
          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   covar=matrix(0,NCOVMAX,1,n);        /*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]); */
   cptcovn=0;        if(globpr){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
   ncovmodel=2+cptcovn;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   /* Read guess parameters */            llt +=ll[k]*gipmx/gsw;
   /* Reads comments: lines beginning with '#' */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);          fprintf(ficresilk," %10.6f\n", -llt);
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      } /* end of wave */
     fputs(line,ficparo);    } /* end of individual */
   }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   ungetc(c,ficpar);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    if(globpr==0){ /* First time we count the contributions and weights */
     for(i=1; i <=nlstate; i++)      gipmx=ipmx;
     for(j=1; j <=nlstate+ndeath-1; j++){      gsw=sw;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    }
       fprintf(ficparo,"%1d%1d",i1,j1);    return -l;
       printf("%1d%1d",i,j);  }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);  /*************** function likelione ***********/
         fprintf(ficparo," %lf",param[i][j][k]);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       }  {
       fscanf(ficpar,"\n");    /* This routine should help understanding what is done with 
       printf("\n");       the selection of individuals/waves and
       fprintf(ficparo,"\n");       to check the exact contribution to the likelihood.
     }       Plotting could be done.
       */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    int k;
   
   p=param[1][1];    if(*globpri !=0){ /* Just counts and sums, no printings */
        strcpy(fileresilk,"ilk"); 
   /* Reads comments: lines beginning with '#' */      strcat(fileresilk,fileres);
   while((c=getc(ficpar))=='#' && c!= EOF){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     ungetc(c,ficpar);        printf("Problem with resultfile: %s\n", fileresilk);
     fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     puts(line);      }
     fputs(line,ficparo);      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
   }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   ungetc(c,ficpar);      /*  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(k=1; k<=nlstate; k++) 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   for(i=1; i <=nlstate; i++){    }
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    *fretone=(*funcone)(p);
       printf("%1d%1d",i,j);    if(*globpri !=0){
       fprintf(ficparo,"%1d%1d",i1,j1);      fclose(ficresilk);
       for(k=1; k<=ncovmodel;k++){      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         fscanf(ficpar,"%le",&delti3[i][j][k]);      fflush(fichtm); 
         printf(" %le",delti3[i][j][k]);    } 
         fprintf(ficparo," %le",delti3[i][j][k]);    return;
       }  }
       fscanf(ficpar,"\n");  
       printf("\n");  
       fprintf(ficparo,"\n");  /*********** Maximum Likelihood Estimation ***************/
     }  
   }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   delti=delti3[1][1];  {
      int i,j, iter=0;
   /* Reads comments: lines beginning with '#' */    double **xi;
   while((c=getc(ficpar))=='#' && c!= EOF){    double fret;
     ungetc(c,ficpar);    double fretone; /* Only one call to likelihood */
     fgets(line, MAXLINE, ficpar);    /*  char filerespow[FILENAMELENGTH];*/
     puts(line);  
     fputs(line,ficparo);  #ifdef NLOPT
   }    int creturn;
   ungetc(c,ficpar);    nlopt_opt opt;
      /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   matcov=matrix(1,npar,1,npar);    double *lb;
   for(i=1; i <=npar; i++){    double minf; /* the minimum objective value, upon return */
     fscanf(ficpar,"%s",&str);    double * p1; /* Shifted parameters from 0 instead of 1 */
     printf("%s",str);    myfunc_data dinst, *d = &dinst;
     fprintf(ficparo,"%s",str);  #endif
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);    xi=matrix(1,npar,1,npar);
       fprintf(ficparo," %.5le",matcov[i][j]);    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++)
     fscanf(ficpar,"\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     fprintf(ficparo,"\n");    strcpy(filerespow,"pow"); 
   }    strcat(filerespow,fileres);
   for(i=1; i <=npar; i++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for(j=i+1;j<=npar;j++)      printf("Problem with resultfile: %s\n", filerespow);
       matcov[i][j]=matcov[j][i];      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
        }
   printf("\n");    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
     /*-------- data file ----------*/        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     if((ficres =fopen(fileres,"w"))==NULL) {    fprintf(ficrespow,"\n");
       printf("Problem with resultfile: %s\n", fileres);goto end;  #ifdef POWELL
     }    powell(p,xi,npar,ftol,&iter,&fret,func);
     fprintf(ficres,"#%s\n",version);  #endif
      
     if((fic=fopen(datafile,"r"))==NULL)    {  #ifdef NLOPT
       printf("Problem with datafile: %s\n", datafile);goto end;  #ifdef NEWUOA
     }    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
     n= lastobs;    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
     severity = vector(1,maxwav);  #endif
     outcome=imatrix(1,maxwav+1,1,n);    lb=vector(0,npar-1);
     num=ivector(1,n);    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     moisnais=vector(1,n);    nlopt_set_lower_bounds(opt, lb);
     annais=vector(1,n);    nlopt_set_initial_step1(opt, 0.1);
     moisdc=vector(1,n);    
     andc=vector(1,n);    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     agedc=vector(1,n);    d->function = func;
     cod=ivector(1,n);    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     weight=vector(1,n);    nlopt_set_min_objective(opt, myfunc, d);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    nlopt_set_xtol_rel(opt, ftol);
     mint=matrix(1,maxwav,1,n);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
     anint=matrix(1,maxwav,1,n);      printf("nlopt failed! %d\n",creturn); 
     s=imatrix(1,maxwav+1,1,n);    }
     adl=imatrix(1,maxwav+1,1,n);        else {
     tab=ivector(1,NCOVMAX);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
     ncodemax=ivector(1,8);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
     i=1;    }
     while (fgets(line, MAXLINE, fic) != NULL)    {    nlopt_destroy(opt);
       if ((i >= firstobs) && (i <=lastobs)) {  #endif
            free_matrix(xi,1,npar,1,npar);
         for (j=maxwav;j>=1;j--){    fclose(ficrespow);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
           strcpy(line,stra);    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  }
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  /**** Computes Hessian and covariance matrix ***/
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    double  **a,**y,*x,pd;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    double **hess;
     int i, j;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    int *indx;
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         }    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         num[i]=atol(stra);    void lubksb(double **a, int npar, int *indx, double b[]) ;
            void ludcmp(double **a, int npar, int *indx, double *d) ;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    double gompertz(double p[]);
           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;}*/    hess=matrix(1,npar,1,npar);
   
         i=i+1;    printf("\nCalculation of the hessian matrix. Wait...\n");
       }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     }    for (i=1;i<=npar;i++){
     /* printf("ii=%d", ij);      printf("%d",i);fflush(stdout);
        scanf("%d",i);*/      fprintf(ficlog,"%d",i);fflush(ficlog);
   imx=i-1; /* Number of individuals */     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   /* for (i=1; i<=imx; i++){      
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      /*  printf(" %f ",p[i]);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    }
     }    
     for (i=1;i<=npar;i++) {
     for (i=1; i<=imx; i++)      for (j=1;j<=npar;j++)  {
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
   /* Calculation of the number of parameter from char model*/          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   Tvar=ivector(1,15);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   Tprod=ivector(1,15);          
   Tvaraff=ivector(1,15);          hess[j][i]=hess[i][j];    
   Tvard=imatrix(1,15,1,2);          /*printf(" %lf ",hess[i][j]);*/
   Tage=ivector(1,15);              }
          }
   if (strlen(model) >1){    }
     j=0, j1=0, k1=1, k2=1;    printf("\n");
     j=nbocc(model,'+');    fprintf(ficlog,"\n");
     j1=nbocc(model,'*');  
     cptcovn=j+1;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     cptcovprod=j1;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
        
        a=matrix(1,npar,1,npar);
     strcpy(modelsav,model);    y=matrix(1,npar,1,npar);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    x=vector(1,npar);
       printf("Error. Non available option model=%s ",model);    indx=ivector(1,npar);
       goto end;    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
        ludcmp(a,npar,indx,&pd);
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');    for (j=1;j<=npar;j++) {
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      for (i=1;i<=npar;i++) x[i]=0;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      x[j]=1;
       /*scanf("%d",i);*/      lubksb(a,npar,indx,x);
       if (strchr(strb,'*')) {      for (i=1;i<=npar;i++){ 
         cutv(strd,strc,strb,'*');        matcov[i][j]=x[i];
         if (strcmp(strc,"age")==0) {      }
           cptcovprod--;    }
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);    printf("\n#Hessian matrix#\n");
           cptcovage++;    fprintf(ficlog,"\n#Hessian matrix#\n");
             Tage[cptcovage]=i;    for (i=1;i<=npar;i++) { 
             /*printf("stre=%s ", stre);*/      for (j=1;j<=npar;j++) { 
         }        printf("%.3e ",hess[i][j]);
         else if (strcmp(strd,"age")==0) {        fprintf(ficlog,"%.3e ",hess[i][j]);
           cptcovprod--;      }
           cutv(strb,stre,strc,'V');      printf("\n");
           Tvar[i]=atoi(stre);      fprintf(ficlog,"\n");
           cptcovage++;    }
           Tage[cptcovage]=i;  
         }    /* Recompute Inverse */
         else {    for (i=1;i<=npar;i++)
           cutv(strb,stre,strc,'V');      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           Tvar[i]=ncov+k1;    ludcmp(a,npar,indx,&pd);
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;    /*  printf("\n#Hessian matrix recomputed#\n");
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);    for (j=1;j<=npar;j++) {
           Tvar[cptcovn+k2]=Tvard[k1][1];      for (i=1;i<=npar;i++) x[i]=0;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      x[j]=1;
           for (k=1; k<=lastobs;k++)      lubksb(a,npar,indx,x);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      for (i=1;i<=npar;i++){ 
           k1++;        y[i][j]=x[i];
           k2=k2+2;        printf("%.3e ",y[i][j]);
         }        fprintf(ficlog,"%.3e ",y[i][j]);
       }      }
       else {      printf("\n");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      fprintf(ficlog,"\n");
        /*  scanf("%d",i);*/    }
       cutv(strd,strc,strb,'V');    */
       Tvar[i]=atoi(strc);  
       }    free_matrix(a,1,npar,1,npar);
       strcpy(modelsav,stra);      free_matrix(y,1,npar,1,npar);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    free_vector(x,1,npar);
         scanf("%d",i);*/    free_ivector(indx,1,npar);
     }    free_matrix(hess,1,npar,1,npar);
 }  
    
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  }
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/  /*************** hessian matrix ****************/
     fclose(fic);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
     /*  if(mle==1){*/    int i;
     if (weightopt != 1) { /* Maximisation without weights*/    int l=1, lmax=20;
       for(i=1;i<=n;i++) weight[i]=1.0;    double k1,k2;
     }    double p2[MAXPARM+1]; /* identical to x */
     /*-calculation of age at interview from date of interview and age at death -*/    double res;
     agev=matrix(1,maxwav,1,imx);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
    for (i=1; i<=imx; i++)    int k=0,kmax=10;
      for(m=2; (m<= maxwav); m++)    double l1;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;    fx=func(x);
          s[m][i]=-1;    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);
     for (i=1; i<=imx; i++)  {      delts=delt;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      for(k=1 ; k <kmax; k=k+1){
       for(m=1; (m<= maxwav); m++){        delt = delta*(l1*k);
         if(s[m][i] >0){        p2[theta]=x[theta] +delt;
           if (s[m][i] == nlstate+1) {        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
             if(agedc[i]>0)        p2[theta]=x[theta]-delt;
               if(moisdc[i]!=99 && andc[i]!=9999)        k2=func(p2)-fx;
               agev[m][i]=agedc[i];        /*res= (k1-2.0*fx+k2)/delt/delt; */
             else {        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
               if (andc[i]!=9999){        
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  #ifdef DEBUGHESS
               agev[m][i]=-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(fabs(k1-2.0*fx+k2) <1.e-13){ */
           else if(s[m][i] !=9){ /* Should no more exist */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          k=kmax;
             if(mint[m][i]==99 || anint[m][i]==9999)        }
               agev[m][i]=1;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             else if(agev[m][i] <agemin){          k=kmax; l=lmax*10;
               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((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             }          delts=delt;
             else if(agev[m][i] >agemax){        }
               agemax=agev[m][i];      }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    }
             }    delti[theta]=delts;
             /*agev[m][i]=anint[m][i]-annais[i];*/    return res; 
             /*   agev[m][i] = age[i]+2*m;*/    
           }  }
           else { /* =9 */  
             agev[m][i]=1;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
             s[m][i]=-1;  {
           }    int i;
         }    int l=1, lmax=20;
         else /*= 0 Unknown */    double k1,k2,k3,k4,res,fx;
           agev[m][i]=1;    double p2[MAXPARM+1];
       }    int k;
      
     }    fx=func(x);
     for (i=1; i<=imx; i++)  {    for (k=1; k<=2; k++) {
       for(m=1; (m<= maxwav); m++){      for (i=1;i<=npar;i++) p2[i]=x[i];
         if (s[m][i] > (nlstate+ndeath)) {      p2[thetai]=x[thetai]+delti[thetai]/k;
           printf("Error: Wrong value in nlstate or ndeath\n");        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           goto end;      k1=func(p2)-fx;
         }    
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    
       p2[thetai]=x[thetai]-delti[thetai]/k;
     free_vector(severity,1,maxwav);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     free_imatrix(outcome,1,maxwav+1,1,n);      k3=func(p2)-fx;
     free_vector(moisnais,1,n);    
     free_vector(annais,1,n);      p2[thetai]=x[thetai]-delti[thetai]/k;
     /* free_matrix(mint,1,maxwav,1,n);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        free_matrix(anint,1,maxwav,1,n);*/      k4=func(p2)-fx;
     free_vector(moisdc,1,n);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     free_vector(andc,1,n);  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
          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);
     wav=ivector(1,imx);  #endif
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    return res;
      }
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   { 
       Tcode=ivector(1,100);    int i,imax,j,k; 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    double big,dum,sum,temp; 
       ncodemax[1]=1;    double *vv; 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);   
          vv=vector(1,n); 
    codtab=imatrix(1,100,1,10);    *d=1.0; 
    h=0;    for (i=1;i<=n;i++) { 
    m=pow(2,cptcoveff);      big=0.0; 
        for (j=1;j<=n;j++) 
    for(k=1;k<=cptcoveff; k++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
      for(i=1; i <=(m/pow(2,k));i++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
        for(j=1; j <= ncodemax[k]; j++){      vv[i]=1.0/big; 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    } 
            h++;    for (j=1;j<=n;j++) { 
            if (h>m) h=1;codtab[h][k]=j;      for (i=1;i<j;i++) { 
          }        sum=a[i][j]; 
        }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      }        a[i][j]=sum; 
    }      } 
       big=0.0; 
       for (i=j;i<=n;i++) { 
    /*for(i=1; i <=m ;i++){        sum=a[i][j]; 
      for(k=1; k <=cptcovn; k++){        for (k=1;k<j;k++) 
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          sum -= a[i][k]*a[k][j]; 
      }        a[i][j]=sum; 
      printf("\n");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
    }          big=dum; 
    scanf("%d",i);*/          imax=i; 
            } 
    /* Calculates basic frequencies. Computes observed prevalence at single age      } 
        and prints on file fileres'p'. */      if (j != imax) { 
         for (k=1;k<=n;k++) { 
              dum=a[imax][k]; 
              a[imax][k]=a[j][k]; 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          a[j][k]=dum; 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        } 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        *d = -(*d); 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        vv[imax]=vv[j]; 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      } 
            indx[j]=imax; 
     /* For Powell, parameters are in a vector p[] starting at p[1]      if (a[j][j] == 0.0) a[j][j]=TINY; 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      if (j != n) { 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     if(mle==1){      } 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    } 
     }    free_vector(vv,1,n);  /* Doesn't work */
      ;
     /*--------- results files --------------*/  } 
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);  
    void lubksb(double **a, int n, int *indx, double b[]) 
   { 
    jk=1;    int i,ii=0,ip,j; 
    fprintf(ficres,"# Parameters\n");    double sum; 
    printf("# Parameters\n");   
    for(i=1,jk=1; i <=nlstate; i++){    for (i=1;i<=n;i++) { 
      for(k=1; k <=(nlstate+ndeath); k++){      ip=indx[i]; 
        if (k != i)      sum=b[ip]; 
          {      b[ip]=b[i]; 
            printf("%d%d ",i,k);      if (ii) 
            fprintf(ficres,"%1d%1d ",i,k);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
            for(j=1; j <=ncovmodel; j++){      else if (sum) ii=i; 
              printf("%f ",p[jk]);      b[i]=sum; 
              fprintf(ficres,"%f ",p[jk]);    } 
              jk++;    for (i=n;i>=1;i--) { 
            }      sum=b[i]; 
            printf("\n");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
            fprintf(ficres,"\n");      b[i]=sum/a[i][i]; 
          }    } 
      }  } 
    }  
  if(mle==1){  void pstamp(FILE *fichier)
     /* Computing hessian and covariance matrix */  {
     ftolhess=ftol; /* Usually correct */    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     hesscov(matcov, p, npar, delti, ftolhess, func);  }
  }  
     fprintf(ficres,"# Scales\n");  /************ Frequencies ********************/
     printf("# Scales\n");  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[])
      for(i=1,jk=1; i <=nlstate; i++){  {  /* Some frequencies */
       for(j=1; j <=nlstate+ndeath; j++){    
         if (j!=i) {    int i, m, jk, j1, bool, z1,j;
           fprintf(ficres,"%1d%1d",i,j);    int first;
           printf("%1d%1d",i,j);    double ***freq; /* Frequencies */
           for(k=1; k<=ncovmodel;k++){    double *pp, **prop;
             printf(" %.5e",delti[jk]);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
             fprintf(ficres," %.5e",delti[jk]);    char fileresp[FILENAMELENGTH];
             jk++;    
           }    pp=vector(1,nlstate);
           printf("\n");    prop=matrix(1,nlstate,iagemin,iagemax+3);
           fprintf(ficres,"\n");    strcpy(fileresp,"p");
         }    strcat(fileresp,fileres);
       }    if((ficresp=fopen(fileresp,"w"))==NULL) {
      }      printf("Problem with prevalence resultfile: %s\n", fileresp);
          fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     k=1;      exit(0);
     fprintf(ficres,"# Covariance\n");    }
     printf("# Covariance\n");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     for(i=1;i<=npar;i++){    j1=0;
       /*  if (k>nlstate) k=1;    
       i1=(i-1)/(ncovmodel*nlstate)+1;    j=cptcoveff;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);    first=1;
       printf("%3d",i);  
       for(j=1; j<=i;j++){    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
         fprintf(ficres," %.5e",matcov[i][j]);    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
         printf(" %.5e",matcov[i][j]);    /*    j1++; */
       }    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       fprintf(ficres,"\n");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       printf("\n");          scanf("%d", i);*/
       k++;        for (i=-5; i<=nlstate+ndeath; i++)  
     }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
                for(m=iagemin; m <= iagemax+3; m++)
     while((c=getc(ficpar))=='#' && c!= EOF){              freq[i][jk][m]=0;
       ungetc(c,ficpar);        
       fgets(line, MAXLINE, ficpar);        for (i=1; i<=nlstate; i++)  
       puts(line);          for(m=iagemin; m <= iagemax+3; m++)
       fputs(line,ficparo);            prop[i][m]=0;
     }        
     ungetc(c,ficpar);        dateintsum=0;
          k2cpt=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        for (i=1; i<=imx; i++) {
              bool=1;
     if (fage <= 2) {          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
       bage = agemin;            for (z1=1; z1<=cptcoveff; z1++)       
       fage = agemax;              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 */
                    bool=0;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                /* 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", 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
                  /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
     while((c=getc(ficpar))=='#' && c!= EOF){              } 
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);   
     puts(line);          if (bool==1){
     fputs(line,ficparo);            for(m=firstpass; m<=lastpass; m++){
   }              k2=anint[m][i]+(mint[m][i]/12.);
   ungetc(c,ficpar);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                if (m<lastpass) {
                        freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   while((c=getc(ficpar))=='#' && c!= EOF){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     ungetc(c,ficpar);                }
     fgets(line, MAXLINE, ficpar);                
     puts(line);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     fputs(line,ficparo);                  dateintsum=dateintsum+k2;
   }                  k2cpt++;
   ungetc(c,ficpar);                }
                  /*}*/
             }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        } /* end i */
          
   fscanf(ficpar,"pop_based=%d\n",&popbased);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
    fprintf(ficparo,"pop_based=%d\n",popbased);          pstamp(ficresp);
    fprintf(ficres,"pop_based=%d\n",popbased);          if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
   while((c=getc(ficpar))=='#' && c!= EOF){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     ungetc(c,ficpar);          fprintf(ficresp, "**********\n#");
     fgets(line, MAXLINE, ficpar);          fprintf(ficlog, "\n#********** Variable "); 
     puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fputs(line,ficparo);          fprintf(ficlog, "**********\n#");
   }        }
   ungetc(c,ficpar);        for(i=1; i<=nlstate;i++) 
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mob_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        fprintf(ficresp, "\n");
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        
         for(i=iagemin; i <= iagemax+3; i++){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);          if(i==iagemax+3){
             fprintf(ficlog,"Total");
 /*------------ gnuplot -------------*/          }else{
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);            if(first==1){
                first=0;
 /*------------ free_vector  -------------*/              printf("See log file for details...\n");
  chdir(path);            }
              fprintf(ficlog,"Age %d", i);
  free_ivector(wav,1,imx);          }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          for(jk=1; jk <=nlstate ; jk++){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
  free_ivector(num,1,n);              pp[jk] += freq[jk][m][i]; 
  free_vector(agedc,1,n);          }
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          for(jk=1; jk <=nlstate ; jk++){
  fclose(ficparo);            for(m=-1, pos=0; m <=0 ; m++)
  fclose(ficres);              pos += freq[jk][m][i];
              if(pp[jk]>=1.e-10){
   /* Reads comments: lines beginning with '#' */              if(first==1){
   while((c=getc(ficpar))=='#' && c!= EOF){                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     puts(line);            }else{
     fputs(line,ficparo);              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   ungetc(c,ficpar);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          }
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);  
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          for(jk=1; jk <=nlstate ; jk++){
 /*--------- index.htm --------*/            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
              pos += pp[jk];
   /*--------------- Prevalence limit --------------*/            posprop += prop[jk][i];
            }
   strcpy(filerespl,"pl");          for(jk=1; jk <=nlstate ; jk++){
   strcat(filerespl,fileres);            if(pos>=1.e-5){
   if((ficrespl=fopen(filerespl,"w"))==NULL) {              if(first==1)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            }else{
   fprintf(ficrespl,"#Prevalence limit\n");              if(first==1)
   fprintf(ficrespl,"#Age ");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficrespl,"\n");            }
              if( i <= iagemax){
   prlim=matrix(1,nlstate,1,nlstate);              if(pos>=1.e-5){
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                /*probs[i][jk][j1]= pp[jk]/pos;*/
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              else
   k=0;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   agebase=agemin;            }
   agelim=agemax;          }
   ftolpl=1.e-10;          
   i1=cptcoveff;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   if (cptcovn < 1){i1=1;}            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   for(cptcov=1;cptcov<=i1;cptcov++){              if(first==1)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         k=k+1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/              }
         fprintf(ficrespl,"\n#******");          if(i <= iagemax)
         for(j=1;j<=cptcoveff;j++)            fprintf(ficresp,"\n");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          if(first==1)
         fprintf(ficrespl,"******\n");            printf("Others in log...\n");
                  fprintf(ficlog,"\n");
         for (age=agebase; age<=agelim; age++){        }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        /*}*/
           fprintf(ficrespl,"%.0f",age );    }
           for(i=1; i<=nlstate;i++)    dateintmean=dateintsum/k2cpt; 
           fprintf(ficrespl," %.5f", prlim[i][i]);   
           fprintf(ficrespl,"\n");    fclose(ficresp);
         }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       }    free_vector(pp,1,nlstate);
     }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   fclose(ficrespl);    /* End of Freq */
   }
   /*------------- h Pij x at various ages ------------*/  
    /************ Prevalence ********************/
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   }       in each health status at the date of interview (if between dateprev1 and dateprev2).
   printf("Computing pij: result on file '%s' \n", filerespij);       We still use firstpass and lastpass as another selection.
      */
   stepsize=(int) (stepm+YEARM-1)/YEARM;   
   /*if (stepm<=24) stepsize=2;*/    int i, m, jk, j1, bool, z1,j;
   
   agelim=AGESUP;    double **prop;
   hstepm=stepsize*YEARM; /* Every year of age */    double posprop; 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    double  y2; /* in fractional years */
      int iagemin, iagemax;
   k=0;    int first; /** to stop verbosity which is redirected to log file */
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    iagemin= (int) agemin;
       k=k+1;    iagemax= (int) agemax;
         fprintf(ficrespij,"\n#****** ");    /*pp=vector(1,nlstate);*/
         for(j=1;j<=cptcoveff;j++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         fprintf(ficrespij,"******\n");    j1=0;
            
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    /*j=cptcoveff;*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    first=1;
           oldm=oldms;savm=savms;    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /*for(i1=1; i1<=ncodemax[k1];i1++){
           fprintf(ficrespij,"# Age");        j1++;*/
           for(i=1; i<=nlstate;i++)        
             for(j=1; j<=nlstate+ndeath;j++)        for (i=1; i<=nlstate; i++)  
               fprintf(ficrespij," %1d-%1d",i,j);          for(m=iagemin; m <= iagemax+3; m++)
           fprintf(ficrespij,"\n");            prop[i][m]=0.0;
           for (h=0; h<=nhstepm; h++){       
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        for (i=1; i<=imx; i++) { /* Each individual */
             for(i=1; i<=nlstate;i++)          bool=1;
               for(j=1; j<=nlstate+ndeath;j++)          if  (cptcovn>0) {
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            for (z1=1; z1<=cptcoveff; z1++) 
             fprintf(ficrespij,"\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           }                bool=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } 
           fprintf(ficrespij,"\n");          if (bool==1) { 
         }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                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); 
   fclose(ficrespij);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   if(stepm == 1) {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   /*---------- Forecasting ------------------*/                  prop[s[m][i]][iagemax+3] += weight[i]; 
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;                } 
               }
   /*printf("calage= %f", calagedate);*/            } /* end selection of waves */
            }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }
         for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   strcpy(fileresf,"f");            posprop += prop[jk][i]; 
   strcat(fileresf,fileres);          } 
   if((ficresf=fopen(fileresf,"w"))==NULL) {          
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;          for(jk=1; jk <=nlstate ; jk++){     
   }            if( i <=  iagemax){ 
   printf("Computing forecasting: result on file '%s' \n", fileresf);              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
   free_matrix(mint,1,maxwav,1,n);              } else{
   free_matrix(anint,1,maxwav,1,n);                if(first==1){
   free_matrix(agev,1,maxwav,1,imx);                  first=0;
                   printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
   /* Mobile average */                }
               }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            } 
           }/* end jk */ 
   if (mobilav==1) {        }/* end i */ 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /*} *//* end i1 */
     movingaverage(agedeb, fage, agemin, mobaverage);    } /* end j1 */
   }    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*free_vector(pp,1,nlstate);*/
   if (stepm<=12) stepsize=1;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   agelim=AGESUP;  
   /*hstepm=stepsize*YEARM; *//* Every year of age */  /************* Waves Concatenation ***************/
   hstepm=1;  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */  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)
   yp1=modf(dateintmean,&yp);  {
   anprojmean=yp;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   yp2=modf((yp1*12),&yp);       Death is a valid wave (if date is known).
   mprojmean=yp;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   yp1=modf((yp2*30.5),&yp);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   jprojmean=yp;       and mw[mi+1][i]. dh depends on stepm.
   if(jprojmean==0) jprojmean=1;       */
   if(mprojmean==0) jprojmean=1;  
     int i, mi, m;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
   if (popforecast==1) {    int first;
     if((ficpop=fopen(popfile,"r"))==NULL)    {    int j, k=0,jk, ju, jl;
       printf("Problem with population file : %s\n",popfile);goto end;    double sum=0.;
     }    first=0;
     popage=ivector(0,AGESUP);    jmin=100000;
     popeffectif=vector(0,AGESUP);    jmax=-1;
     popcount=vector(0,AGESUP);    jmean=0.;
     for(i=1; i<=imx; i++){
     i=1;        mi=0;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)      m=firstpass;
       {      while(s[m][i] <= nlstate){
         i=i+1;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       }          mw[++mi][i]=m;
     imx=i;        if(m >=lastpass)
              break;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        else
   }          m++;
       }/* end while */
   for(cptcov=1;cptcov<=i1;cptcov++){      if (s[m][i] > nlstate){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        mi++;     /* Death is another wave */
       k=k+1;        /* if(mi==0)  never been interviewed correctly before death */
       fprintf(ficresf,"\n#******");           /* Only death is a correct wave */
       for(j=1;j<=cptcoveff;j++) {        mw[mi][i]=m;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }
       }  
       fprintf(ficresf,"******\n");      wav[i]=mi;
       fprintf(ficresf,"# StartingAge FinalAge");      if(mi==0){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        nbwarn++;
       if (popforecast==1)  fprintf(ficresf," [Population]");        if(first==0){
                printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
      for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          first=1;
         fprintf(ficresf,"\n");        }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          if(first==1){
           fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        }
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      } /* end mi==0 */
         nhstepm = nhstepm/hstepm;    } /* End individuals */
          
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1; i<=imx; i++){
         oldm=oldms;savm=savms;      for(mi=1; mi<wav[i];mi++){
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          if (stepm <=0)
                  dh[mi][i]=1;
         for (h=0; h<=nhstepm; h++){        else{
           if (h==(int) (calagedate+YEARM*cpt)) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);            if (agedc[i] < 2*AGESUP) {
           }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           for(j=1; j<=nlstate+ndeath;j++) {              if(j==0) j=1;  /* Survives at least one month after exam */
             kk1=0.;kk2=0;              else if(j<0){
             for(i=1; i<=nlstate;i++) {                        nberr++;
               if (mobilav==1)                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]);
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                j=1; /* Temporary Dangerous patch */
               else {                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);
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                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);
               }              }
               k=k+1;
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];              if (j >= jmax){
             }                jmax=j;
                          ijmax=i;
             if (h==(int)(calagedate+12*cpt)){              }
               fprintf(ficresf," %.3f", kk1);              if (j <= jmin){
                              jmin=j;
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);                ijmin=i;
             }              }
           }              sum=sum+j;
         }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         }            }
      }          }
     }          else{
   }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   
   if (popforecast==1) {            k=k+1;
     free_ivector(popage,0,AGESUP);            if (j >= jmax) {
     free_vector(popeffectif,0,AGESUP);              jmax=j;
     free_vector(popcount,0,AGESUP);              ijmax=i;
   }            }
   free_imatrix(s,1,maxwav+1,1,n);            else if (j <= jmin){
   free_vector(weight,1,n);              jmin=j;
   fclose(ficresf);              ijmin=i;
   }/* End forecasting */            }
   else{            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     erreur=108;            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);            if(j<0){
               nberr++;
   }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               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]);
              }
   /*---------- Health expectancies and variances ------------*/            sum=sum+j;
           }
   strcpy(filerest,"t");          jk= j/stepm;
   strcat(filerest,fileres);          jl= j -jk*stepm;
   if((ficrest=fopen(filerest,"w"))==NULL) {          ju= j -(jk+1)*stepm;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   }            if(jl==0){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);              dh[mi][i]=jk;
               bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
   strcpy(filerese,"e");                    * to avoid the price of an extra matrix product in likelihood */
   strcat(filerese,fileres);              dh[mi][i]=jk+1;
   if((ficreseij=fopen(filerese,"w"))==NULL) {              bh[mi][i]=ju;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            }
   }          }else{
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);            if(jl <= -ju){
               dh[mi][i]=jk;
  strcpy(fileresv,"v");              bh[mi][i]=jl;       /* bias is positive if real duration
   strcat(fileresv,fileres);                                   * is higher than the multiple of stepm and negative otherwise.
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                                   */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);            }
   }            else{
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   k=0;            }
   for(cptcov=1;cptcov<=i1;cptcov++){            if(dh[mi][i]==0){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              dh[mi][i]=1; /* At least one step */
       k=k+1;              bh[mi][i]=ju; /* At least one step */
       fprintf(ficrest,"\n#****** ");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
       for(j=1;j<=cptcoveff;j++)            }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          } /* end if mle */
       fprintf(ficrest,"******\n");        }
       } /* end wave */
       fprintf(ficreseij,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)    jmean=sum/k;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    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(ficreseij,"******\n");    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
    }
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)  /*********** Tricode ****************************/
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
       fprintf(ficresvij,"******\n");  {
     /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
       oldm=oldms;savm=savms;     * Boring subroutine which should only output nbcode[Tvar[j]][k]
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);       * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     * nbcode[Tvar[j]][1]= 
       oldm=oldms;savm=savms;    */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
          int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    int modmaxcovj=0; /* Modality max of covariates j */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    int cptcode=0; /* Modality max of covariates j */
       fprintf(ficrest,"\n");    int modmincovj=0; /* Modality min of covariates j */
          
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;    cptcoveff=0; 
       epj=vector(1,nlstate+1);   
       for(age=bage; age <=fage ;age++){    for (k=-1; k < maxncov; k++) Ndum[k]=0;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)    /* Loop on covariates without age and products */
             prlim[i][i]=probs[(int)age][i][k];    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
         }      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
                                         modality of this covariate Vj*/ 
         fprintf(ficrest," %.0f",age);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                                      * If product of Vn*Vm, still boolean *:
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
           }        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
           epj[nlstate+1] +=epj[j];                                        modality of the nth covariate of individual i. */
         }        if (ij > modmaxcovj)
         for(i=1, vepp=0.;i <=nlstate;i++)          modmaxcovj=ij; 
           for(j=1;j <=nlstate;j++)        else if (ij < modmincovj) 
             vepp += vareij[i][j][(int)age];          modmincovj=ij; 
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        if ((ij < -1) && (ij > NCOVMAX)){
         for(j=1;j <=nlstate;j++){          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          exit(1);
         }        }else
         fprintf(ficrest,"\n");        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       }        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   }        /* getting the maximum value of the modality of the covariate
                   (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                   female is 1, then modmaxcovj=1.*/
       }
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
  fclose(ficreseij);      cptcode=modmaxcovj;
  fclose(ficresvij);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   fclose(ficrest);     /*for (i=0; i<=cptcode; i++) {*/
   fclose(ficpar);      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
   free_vector(epj,1,nlstate+1);        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   /*  scanf("%d ",i); */        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
   /*------- Variance limit prevalence------*/          }
         /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
 strcpy(fileresvpl,"vpl");           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
   strcat(fileresvpl,fileres);      } /* Ndum[-1] number of undefined modalities */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     exit(0);      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   }      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);         modmincovj=3; modmaxcovj = 7;
          There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
  k=0;         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
  for(cptcov=1;cptcov<=i1;cptcov++){         variables V1_1 and V1_2.
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         nbcode[Tvar[j]][ij]=k;
      k=k+1;         nbcode[Tvar[j]][1]=0;
      fprintf(ficresvpl,"\n#****** ");         nbcode[Tvar[j]][2]=1;
      for(j=1;j<=cptcoveff;j++)         nbcode[Tvar[j]][3]=2;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      */
      fprintf(ficresvpl,"******\n");      ij=1; /* ij is similar to i but can jumps over null modalities */
            for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
      oldm=oldms;savm=savms;          /*recode from 0 */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
    }            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
  }                                       k is a modality. If we have model=V1+V1*sex 
                                        then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   fclose(ficresvpl);            ij++;
           }
   /*---------- End : free ----------------*/          if (ij > ncodemax[j]) break; 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        }  /* end of loop on */
        } /* end of loop on modality */ 
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    
     for (k=-1; k< maxncov; k++) Ndum[k]=0; 
      
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);     Ndum[ij]++; 
     } 
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);   ij=1;
     for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      if((Ndum[i]!=0) && (i<=ncovcol)){
   if(erreur >0)       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
     printf("End of Imach with error %d\n",erreur);       Tvaraff[ij]=i; /*For printing (unclear) */
   else   printf("End of Imach\n");       ij++;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */     }else
           Tvaraff[ij]=0;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/   }
   /*printf("Total time was %d uSec.\n", total_usecs);*/   ij--;
   /*------ End -----------*/   cptcoveff=ij; /*Number of total covariates*/
   
   }
  end:  
 #ifdef windows  
   /* chdir(pathcd);*/  /*********** Health Expectancies ****************/
 #endif  
  /*system("wgnuplot graph.plt");*/  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/  {
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    /* Health expectancies, no variances */
  strcpy(plotcmd,GNUPLOTPROGRAM);    int i, j, nhstepm, hstepm, h, nstepm;
  strcat(plotcmd," ");    int nhstepma, nstepma; /* Decreasing with age */
  strcat(plotcmd,optionfilegnuplot);    double age, agelim, hf;
  system(plotcmd);    double ***p3mat;
     double eip;
 #ifdef windows  
   while (z[0] != 'q') {    pstamp(ficreseij);
     chdir(path);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    fprintf(ficreseij,"# Age");
     scanf("%s",z);    for(i=1; i<=nlstate;i++){
     if (z[0] == 'c') system("./imach");      for(j=1; j<=nlstate;j++){
     else if (z[0] == 'e') {        fprintf(ficreseij," e%1d%1d ",i,j);
       chdir(path);      }
       system(optionfilehtm);      fprintf(ficreseij," e%1d. ",i);
     }    }
     else if (z[0] == 'q') exit(0);    fprintf(ficreseij,"\n");
   }  
 #endif    
 }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     agelim=AGESUP;
     /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   
   {
     /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
   
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.25  
changed lines
  Added in v.1.183


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