Diff for /imach/src/imach.c between versions 1.47 and 1.178

version 1.47, 2002/06/10 13:12:01 version 1.178, 2015/01/04 09:35:48
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.178  2015/01/04 09:35:48  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.177  2015/01/03 18:40:56  brouard
   first survey ("cross") where individuals from different ages are    Summary: Still testing ilc32 on OSX
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.176  2015/01/03 16:45:04  brouard
   second wave of interviews ("longitudinal") which measure each change    *** empty log message ***
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.175  2015/01/03 16:33:42  brouard
   model. More health states you consider, more time is necessary to reach the    *** empty log message ***
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.174  2015/01/03 16:15:49  brouard
   probability to be observed in state j at the second wave    Summary: Still in cross-compilation
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.173  2015/01/03 12:06:26  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Summary: trying to detect cross-compilation
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.172  2014/12/27 12:07:47  brouard
   you to do it.  More covariates you add, slower the    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   convergence.  
     Revision 1.171  2014/12/23 13:26:59  brouard
   The advantage of this computer programme, compared to a simple    Summary: Back from Visual C
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Still problem with utsname.h on Windows
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
   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    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.169  2014/12/22 23:08:31  brouard
   semester or year) is model as a multinomial logistic.  The hPx    Summary: 0.98p
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   hPijx.  
     Revision 1.168  2014/12/22 15:17:42  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Summary: update
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.167  2014/12/22 13:50:56  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Summary: Testing uname and compiler version and if compiled 32 or 64
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Testing on Linux 64
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.166  2014/12/22 11:40:47  brouard
   software can be distributed freely for non commercial use. Latest version    *** empty log message ***
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.165  2014/12/16 11:20:36  brouard
      Summary: After compiling on Visual C
 #include <math.h>  
 #include <stdio.h>    * imach.c (Module): Merging 1.61 to 1.162
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.164  2014/12/16 10:52:11  brouard
     Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "gnuplot"    * imach.c (Module): Merging 1.61 to 1.162
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.163  2014/12/16 10:30:11  brouard
 /*#define DEBUG*/    * imach.c (Module): Merging 1.61 to 1.162
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.162  2014/09/25 11:43:39  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Summary: temporary backup 0.99!
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.1  2014/09/16 11:06:58  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: With some code (wrong) for nlopt
   
 #define NINTERVMAX 8    Author:
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.161  2014/09/15 20:41:41  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: Problem with macro SQR on Intel compiler
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.160  2014/09/02 09:24:05  brouard
 #define AGESUP 130    *** empty log message ***
 #define AGEBASE 40  
 #ifdef windows    Revision 1.159  2014/09/01 10:34:10  brouard
 #define DIRSEPARATOR '\\'    Summary: WIN32
 #else    Author: Brouard
 #define DIRSEPARATOR '/'  
 #endif    Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
 char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    Revision 1.157  2014/08/27 16:26:55  brouard
 int nvar;    Summary: Preparing windows Visual studio version
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Author: Brouard
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    In order to compile on Visual studio, time.h is now correct and time_t
 int ndeath=1; /* Number of dead states */    and tm struct should be used. difftime should be used but sometimes I
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    just make the differences in raw time format (time(&now).
 int popbased=0;    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.156  2014/08/25 20:10:10  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    *** empty log message ***
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.155  2014/08/25 18:32:34  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Summary: New compile, minor changes
 double jmean; /* Mean space between 2 waves */    Author: Brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.154  2014/06/20 17:32:08  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Summary: Outputs now all graphs of convergence to period prevalence
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *fichtm; /* Html File */    Revision 1.153  2014/06/20 16:45:46  brouard
 FILE *ficreseij;    Summary: If 3 live state, convergence to period prevalence on same graph
 char filerese[FILENAMELENGTH];    Author: Brouard
 FILE  *ficresvij;  
 char fileresv[FILENAMELENGTH];    Revision 1.152  2014/06/18 17:54:09  brouard
 FILE  *ficresvpl;    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];    Revision 1.151  2014/06/18 16:43:30  brouard
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    *** empty log message ***
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
     Revision 1.150  2014/06/18 16:42:35  brouard
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Revision 1.149  2014/06/18 15:51:14  brouard
 char popfile[FILENAMELENGTH];    Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
     Revision 1.148  2014/06/17 17:38:48  brouard
 #define NR_END 1    Summary: Nothing new
 #define FREE_ARG char*    Author: Brouard
 #define FTOL 1.0e-10  
     Just a new packaging for OS/X version 0.98nS
 #define NRANSI  
 #define ITMAX 200    Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
 #define TOL 2.0e-4  
     Revision 1.146  2014/06/16 10:20:28  brouard
 #define CGOLD 0.3819660    Summary: Merge
 #define ZEPS 1.0e-10    Author: Brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Merge, before building revised version.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.145  2014/06/10 21:23:15  brouard
 #define TINY 1.0e-20    Summary: Debugging with valgrind
     Author: Nicolas Brouard
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Lot of changes in order to output the results with some covariates
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    After the Edimburgh REVES conference 2014, it seems mandatory to
      improve the code.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    No more memory valgrind error but a lot has to be done in order to
 #define rint(a) floor(a+0.5)    continue the work of splitting the code into subroutines.
     Also, decodemodel has been improved. Tricode is still not
 static double sqrarg;    optimal. nbcode should be improved. Documentation has been added in
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    the source code.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.143  2014/01/26 09:45:38  brouard
 int imx;    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Revision 1.142  2014/01/26 03:57:36  brouard
     Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.141  2014/01/26 02:42:01  brouard
 double dateintmean=0;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
 double *weight;    Revision 1.140  2011/09/02 10:37:54  brouard
 int **s; /* Status */    Summary: times.h is ok with mingw32 now.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.138  2010/04/30 18:19:40  brouard
 /**************** split *************************/    *** empty log message ***
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.137  2010/04/29 18:11:38  brouard
    char *s;                             /* pointer */    (Module): Checking covariates for more complex models
    int  l1, l2;                         /* length counters */    than V1+V2. A lot of change to be done. Unstable.
   
    l1 = strlen( path );                 /* length of path */    Revision 1.136  2010/04/26 20:30:53  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): merging some libgsl code. Fixing computation
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */    of likelione (using inter/intrapolation if mle = 0) in order to
    if ( s == NULL ) {                   /* no directory, so use current */    get same likelihood as if mle=1.
 #if     defined(__bsd__)                /* get current working directory */    Some cleaning of code and comments added.
       extern char       *getwd( );  
     Revision 1.135  2009/10/29 15:33:14  brouard
       if ( getwd( dirc ) == NULL ) {    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #else  
       extern char       *getcwd( );    Revision 1.134  2009/10/29 13:18:53  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.133  2009/07/06 10:21:25  brouard
          return( GLOCK_ERROR_GETCWD );    just nforces
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.132  2009/07/06 08:22:05  brouard
    } else {                             /* strip direcotry from path */    Many tings
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.131  2009/06/20 16:22:47  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Some dimensions resccaled
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.130  2009/05/26 06:44:34  brouard
       dirc[l1-l2] = 0;                  /* add zero */    (Module): Max Covariate is now set to 20 instead of 8. A
    }    lot of cleaning with variables initialized to 0. Trying to make
    l1 = strlen( dirc );                 /* length of directory */    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.129  2007/08/31 13:49:27  lievre
 #else    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.128  2006/06/30 13:02:05  brouard
    s = strrchr( name, '.' );            /* find last / */    (Module): Clarifications on computing e.j
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.127  2006/04/28 18:11:50  brouard
    l1= strlen( name);    (Module): Yes the sum of survivors was wrong since
    l2= strlen( s)+1;    imach-114 because nhstepm was no more computed in the age
    strncpy( finame, name, l1-l2);    loop. Now we define nhstepma in the age loop.
    finame[l1-l2]= 0;    (Module): In order to speed up (in case of numerous covariates) we
    return( 0 );                         /* we're done */    compute health expectancies (without variances) in a first step
 }    and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
     computation.
 /******************************************/    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 void replace(char *s, char*t)  
 {    Revision 1.126  2006/04/28 17:23:28  brouard
   int i;    (Module): Yes the sum of survivors was wrong since
   int lg=20;    imach-114 because nhstepm was no more computed in the age
   i=0;    loop. Now we define nhstepma in the age loop.
   lg=strlen(t);    Version 0.98h
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.125  2006/04/04 15:20:31  lievre
     if (t[i]== '\\') s[i]='/';    Errors in calculation of health expectancies. Age was not initialized.
   }    Forecasting file added.
 }  
     Revision 1.124  2006/03/22 17:13:53  lievre
 int nbocc(char *s, char occ)    Parameters are printed with %lf instead of %f (more numbers after the comma).
 {    The log-likelihood is printed in the log file
   int i,j=0;  
   int lg=20;    Revision 1.123  2006/03/20 10:52:43  brouard
   i=0;    * imach.c (Module): <title> changed, corresponds to .htm file
   lg=strlen(s);    name. <head> headers where missing.
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    * imach.c (Module): Weights can have a decimal point as for
   }    English (a comma might work with a correct LC_NUMERIC environment,
   return j;    otherwise the weight is truncated).
 }    Modification of warning when the covariates values are not 0 or
     1.
 void cutv(char *u,char *v, char*t, char occ)    Version 0.98g
 {  
   int i,lg,j,p=0;    Revision 1.122  2006/03/20 09:45:41  brouard
   i=0;    (Module): Weights can have a decimal point as for
   for(j=0; j<=strlen(t)-1; j++) {    English (a comma might work with a correct LC_NUMERIC environment,
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    otherwise the weight is truncated).
   }    Modification of warning when the covariates values are not 0 or
     1.
   lg=strlen(t);    Version 0.98g
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.121  2006/03/16 17:45:01  lievre
   }    * imach.c (Module): Comments concerning covariates added
      u[p]='\0';  
     * imach.c (Module): refinements in the computation of lli if
    for(j=0; j<= lg; j++) {    status=-2 in order to have more reliable computation if stepm is
     if (j>=(p+1))(v[j-p-1] = t[j]);    not 1 month. Version 0.98f
   }  
 }    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 /********************** nrerror ********************/    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 void nrerror(char error_text[])  
 {    Revision 1.119  2006/03/15 17:42:26  brouard
   fprintf(stderr,"ERREUR ...\n");    (Module): Bug if status = -2, the loglikelihood was
   fprintf(stderr,"%s\n",error_text);    computed as likelihood omitting the logarithm. Version O.98e
   exit(1);  
 }    Revision 1.118  2006/03/14 18:20:07  brouard
 /*********************** vector *******************/    (Module): varevsij Comments added explaining the second
 double *vector(int nl, int nh)    table of variances if popbased=1 .
 {    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   double *v;    (Module): Function pstamp added
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    (Module): Version 0.98d
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.117  2006/03/14 17:16:22  brouard
 }    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 /************************ free vector ******************/    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 void free_vector(double*v, int nl, int nh)    (Module): Function pstamp added
 {    (Module): Version 0.98d
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.116  2006/03/06 10:29:27  brouard
     (Module): Variance-covariance wrong links and
 /************************ivector *******************************/    varian-covariance of ej. is needed (Saito).
 int *ivector(long nl,long nh)  
 {    Revision 1.115  2006/02/27 12:17:45  brouard
   int *v;    (Module): One freematrix added in mlikeli! 0.98c
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.114  2006/02/26 12:57:58  brouard
   return v-nl+NR_END;    (Module): Some improvements in processing parameter
 }    filename with strsep.
   
 /******************free ivector **************************/    Revision 1.113  2006/02/24 14:20:24  brouard
 void free_ivector(int *v, long nl, long nh)    (Module): Memory leaks checks with valgrind and:
 {    datafile was not closed, some imatrix were not freed and on matrix
   free((FREE_ARG)(v+nl-NR_END));    allocation too.
 }  
     Revision 1.112  2006/01/30 09:55:26  brouard
 /******************* imatrix *******************************/    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.111  2006/01/25 20:38:18  brouard
 {    (Module): Lots of cleaning and bugs added (Gompertz)
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Module): Comments can be added in data file. Missing date values
   int **m;    can be a simple dot '.'.
    
   /* allocate pointers to rows */    Revision 1.110  2006/01/25 00:51:50  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Module): Lots of cleaning and bugs added (Gompertz)
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.109  2006/01/24 19:37:15  brouard
   m -= nrl;    (Module): Comments (lines starting with a #) are allowed in data.
    
      Revision 1.108  2006/01/19 18:05:42  lievre
   /* allocate rows and set pointers to them */    Gnuplot problem appeared...
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    To be fixed
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.107  2006/01/19 16:20:37  brouard
   m[nrl] -= ncl;    Test existence of gnuplot in imach path
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.106  2006/01/19 13:24:36  brouard
      Some cleaning and links added in html output
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.105  2006/01/05 20:23:19  lievre
 }    *** empty log message ***
   
 /****************** free_imatrix *************************/    Revision 1.104  2005/09/30 16:11:43  lievre
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): sump fixed, loop imx fixed, and simplifications.
       int **m;    (Module): If the status is missing at the last wave but we know
       long nch,ncl,nrh,nrl;    that the person is alive, then we can code his/her status as -2
      /* free an int matrix allocated by imatrix() */    (instead of missing=-1 in earlier versions) and his/her
 {    contributions to the likelihood is 1 - Prob of dying from last
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   free((FREE_ARG) (m+nrl-NR_END));    the healthy state at last known wave). Version is 0.98
 }  
     Revision 1.103  2005/09/30 15:54:49  lievre
 /******************* matrix *******************************/    (Module): sump fixed, loop imx fixed, and simplifications.
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.102  2004/09/15 17:31:30  brouard
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Add the possibility to read data file including tab characters.
   double **m;  
     Revision 1.101  2004/09/15 10:38:38  brouard
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Fix on curr_time
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.100  2004/07/12 18:29:06  brouard
   m -= nrl;    Add version for Mac OS X. Just define UNIX in Makefile
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.99  2004/06/05 08:57:40  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    *** empty log message ***
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    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 matrix ************************/    cross-longitudinal survey is different from the mortality estimated
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    from other sources like vital statistic data.
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    The same imach parameter file can be used but the option for mle should be -3.
   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.
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    The output is very simple: only an estimate of the intercept and of
 {    the slope with 95% confident intervals.
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Current limitations:
     A) Even if you enter covariates, i.e. with the
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   if (!m) nrerror("allocation failure 1 in matrix()");    B) There is no computation of Life Expectancy nor Life Table.
   m += NR_END;  
   m -= nrl;    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    suppressed.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.96  2003/07/15 15:38:55  brouard
   m[nrl] -= ncl;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Revision 1.95  2003/07/08 07:54:34  brouard
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    * imach.c (Repository):
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    (Repository): Using imachwizard code to output a more meaningful covariance
   m[nrl][ncl] += NR_END;    matrix (cov(a12,c31) instead of numbers.
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.94  2003/06/27 13:00:02  brouard
     m[nrl][j]=m[nrl][j-1]+nlay;    Just cleaning
    
   for (i=nrl+1; i<=nrh; i++) {    Revision 1.93  2003/06/25 16:33:55  brouard
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    (Module): On windows (cygwin) function asctime_r doesn't
     for (j=ncl+1; j<=nch; j++)    exist so I changed back to asctime which exists.
       m[i][j]=m[i][j-1]+nlay;    (Module): Version 0.96b
   }  
   return m;    Revision 1.92  2003/06/25 16:30:45  brouard
 }    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Revision 1.91  2003/06/25 15:30:29  brouard
 {    * imach.c (Repository): Duplicated warning errors corrected.
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    (Repository): Elapsed time after each iteration is now output. It
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    helps to forecast when convergence will be reached. Elapsed time
   free((FREE_ARG)(m+nrl-NR_END));    is stamped in powell.  We created a new html file for the graphs
 }    concerning matrix of covariance. It has extension -cov.htm.
   
 /***************** f1dim *************************/    Revision 1.90  2003/06/24 12:34:15  brouard
 extern int ncom;    (Module): Some bugs corrected for windows. Also, when
 extern double *pcom,*xicom;    mle=-1 a template is output in file "or"mypar.txt with the design
 extern double (*nrfunc)(double []);    of the covariance matrix to be input.
    
 double f1dim(double x)    Revision 1.89  2003/06/24 12:30:52  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   int j;    mle=-1 a template is output in file "or"mypar.txt with the design
   double f;    of the covariance matrix to be input.
   double *xt;  
      Revision 1.88  2003/06/23 17:54:56  brouard
   xt=vector(1,ncom);    * 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.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    Revision 1.87  2003/06/18 12:26:01  brouard
   free_vector(xt,1,ncom);    Version 0.96
   return f;  
 }    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 /*****************brent *************************/    routine fileappend.
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {    Revision 1.85  2003/06/17 13:12:43  brouard
   int iter;    * imach.c (Repository): Check when date of death was earlier that
   double a,b,d,etemp;    current date of interview. It may happen when the death was just
   double fu,fv,fw,fx;    prior to the death. In this case, dh was negative and likelihood
   double ftemp;    was wrong (infinity). We still send an "Error" but patch by
   double p,q,r,tol1,tol2,u,v,w,x,xm;    assuming that the date of death was just one stepm after the
   double e=0.0;    interview.
      (Repository): Because some people have very long ID (first column)
   a=(ax < cx ? ax : cx);    we changed int to long in num[] and we added a new lvector for
   b=(ax > cx ? ax : cx);    memory allocation. But we also truncated to 8 characters (left
   x=w=v=bx;    truncation)
   fw=fv=fx=(*f)(x);    (Repository): No more line truncation errors.
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    Revision 1.84  2003/06/13 21:44:43  brouard
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    * imach.c (Repository): Replace "freqsummary" at a correct
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    place. It differs from routine "prevalence" which may be called
     printf(".");fflush(stdout);    many times. Probs is memory consuming and must be used with
 #ifdef DEBUG    parcimony.
     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);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    Revision 1.83  2003/06/10 13:39:11  lievre
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    *** empty log message ***
       *xmin=x;  
       return fx;    Revision 1.82  2003/06/05 15:57:20  brouard
     }    Add log in  imach.c and  fullversion number is now printed.
     ftemp=fu;  
     if (fabs(e) > tol1) {  */
       r=(x-w)*(fx-fv);  /*
       q=(x-v)*(fx-fw);     Interpolated Markov Chain
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);    Short summary of the programme:
       if (q > 0.0) p = -p;    
       q=fabs(q);    This program computes Healthy Life Expectancies from
       etemp=e;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
       e=d;    first survey ("cross") where individuals from different ages are
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    interviewed on their health status or degree of disability (in the
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    case of a health survey which is our main interest) -2- at least a
       else {    second wave of interviews ("longitudinal") which measure each change
         d=p/q;    (if any) in individual health status.  Health expectancies are
         u=x+d;    computed from the time spent in each health state according to a
         if (u-a < tol2 || b-u < tol2)    model. More health states you consider, more time is necessary to reach the
           d=SIGN(tol1,xm-x);    Maximum Likelihood of the parameters involved in the model.  The
       }    simplest model is the multinomial logistic model where pij is the
     } else {    probability to be observed in state j at the second wave
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    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
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    'age' is age and 'sex' is a covariate. If you want to have a more
     fu=(*f)(u);    complex model than "constant and age", you should modify the program
     if (fu <= fx) {    where the markup *Covariates have to be included here again* invites
       if (u >= x) a=x; else b=x;    you to do it.  More covariates you add, slower the
       SHFT(v,w,x,u)    convergence.
         SHFT(fv,fw,fx,fu)  
         } else {    The advantage of this computer programme, compared to a simple
           if (u < x) a=u; else b=u;    multinomial logistic model, is clear when the delay between waves is not
           if (fu <= fw || w == x) {    identical for each individual. Also, if a individual missed an
             v=w;    intermediate interview, the information is lost, but taken into
             w=u;    account using an interpolation or extrapolation.  
             fv=fw;  
             fw=fu;    hPijx is the probability to be observed in state i at age x+h
           } else if (fu <= fv || v == x || v == w) {    conditional to the observed state i at age x. The delay 'h' can be
             v=u;    split into an exact number (nh*stepm) of unobserved intermediate
             fv=fu;    states. This elementary transition (by month, quarter,
           }    semester or year) is modelled as a multinomial logistic.  The hPx
         }    matrix is simply the matrix product of nh*stepm elementary matrices
   }    and the contribution of each individual to the likelihood is simply
   nrerror("Too many iterations in brent");    hPijx.
   *xmin=x;  
   return fx;    Also this programme outputs the covariance matrix of the parameters but also
 }    of the life expectancies. It also computes the period (stable) prevalence. 
     
 /****************** mnbrak ***********************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    This software have been partly granted by Euro-REVES, a concerted action
             double (*func)(double))    from the European Union.
 {    It is copyrighted identically to a GNU software product, ie programme and
   double ulim,u,r,q, dum;    software can be distributed freely for non commercial use. Latest version
   double fu;    can be accessed at http://euroreves.ined.fr/imach .
    
   *fa=(*func)(*ax);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   *fb=(*func)(*bx);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   if (*fb > *fa) {    
     SHFT(dum,*ax,*bx,dum)    **********************************************************************/
       SHFT(dum,*fb,*fa,dum)  /*
       }    main
   *cx=(*bx)+GOLD*(*bx-*ax);    read parameterfile
   *fc=(*func)(*cx);    read datafile
   while (*fb > *fc) {    concatwav
     r=(*bx-*ax)*(*fb-*fc);    freqsummary
     q=(*bx-*cx)*(*fb-*fa);    if (mle >= 1)
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      mlikeli
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    print results files
     ulim=(*bx)+GLIMIT*(*cx-*bx);    if mle==1 
     if ((*bx-u)*(u-*cx) > 0.0) {       computes hessian
       fu=(*func)(u);    read end of parameter file: agemin, agemax, bage, fage, estepm
     } else if ((*cx-u)*(u-ulim) > 0.0) {        begin-prev-date,...
       fu=(*func)(u);    open gnuplot file
       if (fu < *fc) {    open html file
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
           SHFT(*fb,*fc,fu,(*func)(u))     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
           }                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      freexexit2 possible for memory heap.
       u=ulim;  
       fu=(*func)(u);    h Pij x                         | pij_nom  ficrestpij
     } else {     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
       u=(*cx)+GOLD*(*cx-*bx);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
       fu=(*func)(u);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
     }  
     SHFT(*ax,*bx,*cx,u)         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       SHFT(*fa,*fb,*fc,fu)         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       }    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
 /*************** linmin ************************/  
     forecasting if prevfcast==1 prevforecast call prevalence()
 int ncom;    health expectancies
 double *pcom,*xicom;    Variance-covariance of DFLE
 double (*nrfunc)(double []);    prevalence()
       movingaverage()
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    varevsij() 
 {    if popbased==1 varevsij(,popbased)
   double brent(double ax, double bx, double cx,    total life expectancies
                double (*f)(double), double tol, double *xmin);    Variance of period (stable) prevalence
   double f1dim(double x);   end
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  */
               double *fc, double (*func)(double));  
   int j;  #define POWELL /* Instead of NLOPT */
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  #include <math.h>
    #include <stdio.h>
   ncom=n;  #include <stdlib.h>
   pcom=vector(1,n);  #include <string.h>
   xicom=vector(1,n);  
   nrfunc=func;  #ifdef _WIN32
   for (j=1;j<=n;j++) {  #include <io.h>
     pcom[j]=p[j];  #include <windows.h>
     xicom[j]=xi[j];  #include <tchar.h>
   }  #else
   ax=0.0;  #include <unistd.h>
   xx=1.0;  #endif
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #include <limits.h>
 #ifdef DEBUG  #include <sys/types.h>
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  #if defined(__GNUC__)
   for (j=1;j<=n;j++) {  #include <sys/utsname.h> /* Doesn't work on Windows */
     xi[j] *= xmin;  #endif
     p[j] += xi[j];  
   }  #include <sys/stat.h>
   free_vector(xicom,1,n);  #include <errno.h>
   free_vector(pcom,1,n);  /* extern int errno; */
 }  
   /* #ifdef LINUX */
 /*************** powell ************************/  /* #include <time.h> */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /* #include "timeval.h" */
             double (*func)(double []))  /* #else */
 {  /* #include <sys/time.h> */
   void linmin(double p[], double xi[], int n, double *fret,  /* #endif */
               double (*func)(double []));  
   int i,ibig,j;  #include <time.h>
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  #ifdef GSL
   double *xits;  #include <gsl/gsl_errno.h>
   pt=vector(1,n);  #include <gsl/gsl_multimin.h>
   ptt=vector(1,n);  #endif
   xit=vector(1,n);  
   xits=vector(1,n);  
   *fret=(*func)(p);  #ifdef NLOPT
   for (j=1;j<=n;j++) pt[j]=p[j];  #include <nlopt.h>
   for (*iter=1;;++(*iter)) {  typedef struct {
     fp=(*fret);    double (* function)(double [] );
     ibig=0;  } myfunc_data ;
     del=0.0;  #endif
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /* #include <libintl.h> */
       printf(" %d %.12f",i, p[i]);  /* #define _(String) gettext (String) */
     printf("\n");  
     for (i=1;i<=n;i++) {  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  #define GNUPLOTPROGRAM "gnuplot"
 #ifdef DEBUG  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       printf("fret=%lf \n",*fret);  #define FILENAMELENGTH 132
 #endif  
       printf("%d",i);fflush(stdout);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       linmin(p,xit,n,fret,func);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         ibig=i;  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
       }  
 #ifdef DEBUG  #define NINTERVMAX 8
       printf("%d %.12e",i,(*fret));  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       for (j=1;j<=n;j++) {  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
         printf(" x(%d)=%.12e",j,xit[j]);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
       }  #define MAXN 20000
       for(j=1;j<=n;j++)  #define YEARM 12. /**< Number of months per year */
         printf(" p=%.12e",p[j]);  #define AGESUP 130
       printf("\n");  #define AGEBASE 40
 #endif  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
     }  #ifdef _WIN32
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define DIRSEPARATOR '\\'
 #ifdef DEBUG  #define CHARSEPARATOR "\\"
       int k[2],l;  #define ODIRSEPARATOR '/'
       k[0]=1;  #else
       k[1]=-1;  #define DIRSEPARATOR '/'
       printf("Max: %.12e",(*func)(p));  #define CHARSEPARATOR "/"
       for (j=1;j<=n;j++)  #define ODIRSEPARATOR '\\'
         printf(" %.12e",p[j]);  #endif
       printf("\n");  
       for(l=0;l<=1;l++) {  /* $Id$ */
         for (j=1;j<=n;j++) {  /* $State$ */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
         }  char fullversion[]="$Revision$ $Date$"; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  char strstart[80];
       }  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 #endif  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int nvar=0, nforce=0; /* Number of variables, number of forces */
   /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       free_vector(xit,1,n);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
       free_vector(xits,1,n);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
       free_vector(ptt,1,n);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       free_vector(pt,1,n);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       return;  int cptcovprodnoage=0; /**< Number of covariate products without age */   
     }  int cptcoveff=0; /* Total number of covariates to vary for printing results */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  int cptcov=0; /* Working variable */
     for (j=1;j<=n;j++) {  int npar=NPARMAX;
       ptt[j]=2.0*p[j]-pt[j];  int nlstate=2; /* Number of live states */
       xit[j]=p[j]-pt[j];  int ndeath=1; /* Number of dead states */
       pt[j]=p[j];  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     }  int popbased=0;
     fptt=(*func)(ptt);  
     if (fptt < fp) {  int *wav; /* Number of waves for this individuual 0 is possible */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  int maxwav=0; /* Maxim number of waves */
       if (t < 0.0) {  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
         linmin(p,xit,n,fret,func);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
         for (j=1;j<=n;j++) {  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
           xi[j][ibig]=xi[j][n];                     to the likelihood and the sum of weights (done by funcone)*/
           xi[j][n]=xit[j];  int mle=1, weightopt=0;
         }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #ifdef DEBUG  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         for(j=1;j<=n;j++)             * wave mi and wave mi+1 is not an exact multiple of stepm. */
           printf(" %.12e",xit[j]);  int countcallfunc=0;  /* Count the number of calls to func */
         printf("\n");  double jmean=1; /* Mean space between 2 waves */
 #endif  double **matprod2(); /* test */
       }  double **oldm, **newm, **savm; /* Working pointers to matrices */
     }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   }  /*FILE *fic ; */ /* Used in readdata only */
 }  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 /**** Prevalence limit ****************/  int globpr=0; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  long ipmx=0; /* Number of contributions */
 {  double sw; /* Sum of weights */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  char filerespow[FILENAMELENGTH];
      matrix by transitions matrix until convergence is reached */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
   int i, ii,j,k;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   double min, max, maxmin, maxmax,sumnew=0.;  FILE *ficresprobmorprev;
   double **matprod2();  FILE *fichtm, *fichtmcov; /* Html File */
   double **out, cov[NCOVMAX], **pmij();  FILE *ficreseij;
   double **newm;  char filerese[FILENAMELENGTH];
   double agefin, delaymax=50 ; /* Max number of years to converge */  FILE *ficresstdeij;
   char fileresstde[FILENAMELENGTH];
   for (ii=1;ii<=nlstate+ndeath;ii++)  FILE *ficrescveij;
     for (j=1;j<=nlstate+ndeath;j++){  char filerescve[FILENAMELENGTH];
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  FILE  *ficresvij;
     }  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
    cov[1]=1.;  char fileresvpl[FILENAMELENGTH];
    char title[MAXLINE];
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     newm=savm;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     /* Covariates have to be included here again */  char command[FILENAMELENGTH];
      cov[2]=agefin;  int  outcmd=0;
    
       for (k=1; k<=cptcovn;k++) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  char fileregp[FILENAMELENGTH];
       for (k=1; k<=cptcovprod;k++)  char popfile[FILENAMELENGTH];
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  /* struct timezone tzp; */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /* extern int gettimeofday(); */
   struct tm tml, *gmtime(), *localtime();
     savm=oldm;  
     oldm=newm;  extern time_t time();
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       min=1.;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
       max=0.;  struct tm tm;
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  char strcurr[80], strfor[80];
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  char *endptr;
         max=FMAX(max,prlim[i][j]);  long lval;
         min=FMIN(min,prlim[i][j]);  double dval;
       }  
       maxmin=max-min;  #define NR_END 1
       maxmax=FMAX(maxmax,maxmin);  #define FREE_ARG char*
     }  #define FTOL 1.0e-10
     if(maxmax < ftolpl){  
       return prlim;  #define NRANSI 
     }  #define ITMAX 200 
   }  
 }  #define TOL 2.0e-4 
   
 /*************** transition probabilities ***************/  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 {  
   double s1, s2;  #define GOLD 1.618034 
   /*double t34;*/  #define GLIMIT 100.0 
   int i,j,j1, nc, ii, jj;  #define TINY 1.0e-20 
   
     for(i=1; i<= nlstate; i++){  static double maxarg1,maxarg2;
     for(j=1; j<i;j++){  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
         /*s2 += param[i][j][nc]*cov[nc];*/    
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  #define rint(a) floor(a+0.5)
       }  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
       ps[i][j]=s2;  /* #define mytinydouble 1.0e-16 */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
     }  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
     for(j=i+1; j<=nlstate+ndeath;j++){  /* static double dsqrarg; */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  static double sqrarg;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       ps[i][j]=s2;  int agegomp= AGEGOMP;
     }  
   }  int imx; 
     /*ps[3][2]=1;*/  int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
   for(i=1; i<= nlstate; i++){  
      s1=0;  int estepm;
     for(j=1; j<i; j++)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  int m,nb;
       s1+=exp(ps[i][j]);  long *num;
     ps[i][i]=1./(s1+1.);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     for(j=1; j<i; j++)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double **pmmij, ***probs;
     for(j=i+1; j<=nlstate+ndeath; j++)  double *ageexmed,*agecens;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double dateintmean=0;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */  double *weight;
   int **s; /* Status */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  double *agedc;
     for(jj=1; jj<= nlstate+ndeath; jj++){  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       ps[ii][jj]=0;                    * covar=matrix(0,NCOVMAX,1,n); 
       ps[ii][ii]=1;                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
     }  double  idx; 
   }  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Ndum; /** Freq of modality (tricode */
   int **codtab; /**< codtab=imatrix(1,100,1,10); */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     for(jj=1; jj<= nlstate+ndeath; jj++){  double *lsurv, *lpop, *tpop;
      printf("%lf ",ps[ii][jj]);  
    }  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
     printf("\n ");  double ftolhess; /**< Tolerance for computing hessian */
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  /**************** split *************************/
 /*  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  {
   goto end;*/    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     return ps;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 }    */ 
     char  *ss;                            /* pointer */
 /**************** Product of 2 matrices ******************/    int   l1, l2;                         /* length counters */
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    l1 = strlen(path );                   /* length of path */
 {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   /* in, b, out are matrice of pointers which should have been initialized      strcpy( name, path );               /* we got the fullname name because no directory */
      before: only the contents of out is modified. The function returns      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
      a pointer to pointers identical to out */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   long i, j, k;      /* get current working directory */
   for(i=nrl; i<= nrh; i++)      /*    extern  char* getcwd ( char *buf , int len);*/
     for(k=ncolol; k<=ncoloh; k++)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        return( GLOCK_ERROR_GETCWD );
         out[i][k] +=in[i][j]*b[j][k];      }
       /* got dirc from getcwd*/
   return out;      printf(" DIRC = %s \n",dirc);
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 /************* Higher Matrix Product ***************/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      printf(" DIRC2 = %s \n",dirc);
      duration (i.e. until    }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    /* We add a separator at the end of dirc if not exists */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    l1 = strlen( dirc );                  /* length of directory */
      (typically every 2 years instead of every month which is too big).    if( dirc[l1-1] != DIRSEPARATOR ){
      Model is determined by parameters x and covariates have to be      dirc[l1] =  DIRSEPARATOR;
      included manually here.      dirc[l1+1] = 0; 
       printf(" DIRC3 = %s \n",dirc);
      */    }
     ss = strrchr( name, '.' );            /* find last / */
   int i, j, d, h, k;    if (ss >0){
   double **out, cov[NCOVMAX];      ss++;
   double **newm;      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
   /* Hstepm could be zero and should return the unit matrix */      l2= strlen(ss)+1;
   for (i=1;i<=nlstate+ndeath;i++)      strncpy( finame, name, l1-l2);
     for (j=1;j<=nlstate+ndeath;j++){      finame[l1-l2]= 0;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    }
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }    return( 0 );                          /* we're done */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  
       newm=savm;  /******************************************/
       /* Covariates have to be included here again */  
       cov[1]=1.;  void replace_back_to_slash(char *s, char*t)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    int i;
       for (k=1; k<=cptcovage;k++)    int lg=0;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    i=0;
       for (k=1; k<=cptcovprod;k++)    lg=strlen(t);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  }
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  char *trimbb(char *out, char *in)
       savm=oldm;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       oldm=newm;    char *s;
     }    s=out;
     for(i=1; i<=nlstate+ndeath; i++)    while (*in != '\0'){
       for(j=1;j<=nlstate+ndeath;j++) {      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         po[i][j][h]=newm[i][j];        in++;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      }
          */      *out++ = *in++;
       }    }
   } /* end h */    *out='\0';
   return po;    return s;
 }  }
   
   char *cutl(char *blocc, char *alocc, char *in, char occ)
 /*************** log-likelihood *************/  {
 double func( double *x)    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
 {       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   int i, ii, j, k, mi, d, kk;       gives blocc="abcdef2ghi" and alocc="j".
   double l, ll[NLSTATEMAX], cov[NCOVMAX];       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   double **out;    */
   double sw; /* Sum of weights */    char *s, *t;
   double lli; /* Individual log likelihood */    t=in;s=in;
   long ipmx;    while ((*in != occ) && (*in != '\0')){
   /*extern weight */      *alocc++ = *in++;
   /* We are differentiating ll according to initial status */    }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    if( *in == occ){
   /*for(i=1;i<imx;i++)      *(alocc)='\0';
     printf(" %d\n",s[4][i]);      s=++in;
   */    }
   cov[1]=1.;   
     if (s == t) {/* occ not found */
   for(k=1; k<=nlstate; k++) ll[k]=0.;      *(alocc-(in-s))='\0';
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      in=s;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    }
     for(mi=1; mi<= wav[i]-1; mi++){    while ( *in != '\0'){
       for (ii=1;ii<=nlstate+ndeath;ii++)      *blocc++ = *in++;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    }
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;    *blocc='\0';
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return t;
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  char *cutv(char *blocc, char *alocc, char *in, char occ)
         }  {
            /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       gives blocc="abcdef2ghi" and alocc="j".
         savm=oldm;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         oldm=newm;    */
            char *s, *t;
            t=in;s=in;
       } /* end mult */    while (*in != '\0'){
            while( *in == occ){
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        *blocc++ = *in++;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        s=in;
       ipmx +=1;      }
       sw += weight[i];      *blocc++ = *in++;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    }
     } /* end of wave */    if (s == t) /* occ not found */
   } /* end of individual */      *(blocc-(in-s))='\0';
     else
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      *(blocc-(in-s)-1)='\0';
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    in=s;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    while ( *in != '\0'){
   return -l;      *alocc++ = *in++;
 }    }
   
     *alocc='\0';
 /*********** Maximum Likelihood Estimation ***************/    return s;
   }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  int nbocc(char *s, char occ)
   int i,j, iter;  {
   double **xi,*delti;    int i,j=0;
   double fret;    int lg=20;
   xi=matrix(1,npar,1,npar);    i=0;
   for (i=1;i<=npar;i++)    lg=strlen(s);
     for (j=1;j<=npar;j++)    for(i=0; i<= lg; i++) {
       xi[i][j]=(i==j ? 1.0 : 0.0);    if  (s[i] == occ ) j++;
   printf("Powell\n");    }
   powell(p,xi,npar,ftol,&iter,&fret,func);    return j;
   }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /* void cutv(char *u,char *v, char*t, char occ) */
   /* { */
 }  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
 /**** Computes Hessian and covariance matrix ***/  /*      gives u="abcdef2ghi" and v="j" *\/ */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*   int i,lg,j,p=0; */
 {  /*   i=0; */
   double  **a,**y,*x,pd;  /*   lg=strlen(t); */
   double **hess;  /*   for(j=0; j<=lg-1; j++) { */
   int i, j,jk;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   int *indx;  /*   } */
   
   double hessii(double p[], double delta, int theta, double delti[]);  /*   for(j=0; j<p; j++) { */
   double hessij(double p[], double delti[], int i, int j);  /*     (u[j] = t[j]); */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  /*   } */
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /*      u[p]='\0'; */
   
   hess=matrix(1,npar,1,npar);  /*    for(j=0; j<= lg; j++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   printf("\nCalculation of the hessian matrix. Wait...\n");  /*   } */
   for (i=1;i<=npar;i++){  /* } */
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  #ifdef _WIN32
     /*printf(" %f ",p[i]);*/  char * strsep(char **pp, const char *delim)
     /*printf(" %lf ",hess[i][i]);*/  {
   }    char *p, *q;
             
   for (i=1;i<=npar;i++) {    if ((p = *pp) == NULL)
     for (j=1;j<=npar;j++)  {      return 0;
       if (j>i) {    if ((q = strpbrk (p, delim)) != NULL)
         printf(".%d%d",i,j);fflush(stdout);    {
         hess[i][j]=hessij(p,delti,i,j);      *pp = q + 1;
         hess[j][i]=hess[i][j];          *q = '\0';
         /*printf(" %lf ",hess[i][j]);*/    }
       }    else
     }      *pp = 0;
   }    return p;
   printf("\n");  }
   #endif
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
    /********************** nrerror ********************/
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);  void nrerror(char error_text[])
   x=vector(1,npar);  {
   indx=ivector(1,npar);    fprintf(stderr,"ERREUR ...\n");
   for (i=1;i<=npar;i++)    fprintf(stderr,"%s\n",error_text);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    exit(EXIT_FAILURE);
   ludcmp(a,npar,indx,&pd);  }
   /*********************** vector *******************/
   for (j=1;j<=npar;j++) {  double *vector(int nl, int nh)
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    double *v;
     lubksb(a,npar,indx,x);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     for (i=1;i<=npar;i++){    if (!v) nrerror("allocation failure in vector");
       matcov[i][j]=x[i];    return v-nl+NR_END;
     }  }
   }  
   /************************ free vector ******************/
   printf("\n#Hessian matrix#\n");  void free_vector(double*v, int nl, int nh)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++) {    free((FREE_ARG)(v+nl-NR_END));
       printf("%.3e ",hess[i][j]);  }
     }  
     printf("\n");  /************************ivector *******************************/
   }  int *ivector(long nl,long nh)
   {
   /* Recompute Inverse */    int *v;
   for (i=1;i<=npar;i++)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    if (!v) nrerror("allocation failure in ivector");
   ludcmp(a,npar,indx,&pd);    return v-nl+NR_END;
   }
   /*  printf("\n#Hessian matrix recomputed#\n");  
   /******************free ivector **************************/
   for (j=1;j<=npar;j++) {  void free_ivector(int *v, long nl, long nh)
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    free((FREE_ARG)(v+nl-NR_END));
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  /************************lvector *******************************/
       printf("%.3e ",y[i][j]);  long *lvector(long nl,long nh)
     }  {
     printf("\n");    long *v;
   }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   */    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   free_matrix(a,1,npar,1,npar);  }
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);  /******************free lvector **************************/
   free_ivector(indx,1,npar);  void free_lvector(long *v, long nl, long nh)
   free_matrix(hess,1,npar,1,npar);  {
     free((FREE_ARG)(v+nl-NR_END));
   }
 }  
   /******************* imatrix *******************************/
 /*************** hessian matrix ****************/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 double hessii( double x[], double delta, int theta, double delti[])       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 {  { 
   int i;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   int l=1, lmax=20;    int **m; 
   double k1,k2;    
   double p2[NPARMAX+1];    /* allocate pointers to rows */ 
   double res;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double fx;    m += NR_END; 
   int k=0,kmax=10;    m -= nrl; 
   double l1;    
     
   fx=func(x);    /* allocate rows and set pointers to them */ 
   for (i=1;i<=npar;i++) p2[i]=x[i];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   for(l=0 ; l <=lmax; l++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     l1=pow(10,l);    m[nrl] += NR_END; 
     delts=delt;    m[nrl] -= ncl; 
     for(k=1 ; k <kmax; k=k+1){    
       delt = delta*(l1*k);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       p2[theta]=x[theta] +delt;    
       k1=func(p2)-fx;    /* return pointer to array of pointers to rows */ 
       p2[theta]=x[theta]-delt;    return m; 
       k2=func(p2)-fx;  } 
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  /****************** free_imatrix *************************/
        void free_imatrix(m,nrl,nrh,ncl,nch)
 #ifdef DEBUG        int **m;
       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);        long nch,ncl,nrh,nrl; 
 #endif       /* free an int matrix allocated by imatrix() */ 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  { 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         k=kmax;    free((FREE_ARG) (m+nrl-NR_END)); 
       }  } 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  {
         delts=delt;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       }    double **m;
     }  
   }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   delti[theta]=delts;    if (!m) nrerror("allocation failure 1 in matrix()");
   return res;    m += NR_END;
      m -= nrl;
 }  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 double hessij( double x[], double delti[], int thetai,int thetaj)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 {    m[nrl] += NR_END;
   int i;    m[nrl] -= ncl;
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double p2[NPARMAX+1];    return m;
   int k;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   fx=func(x);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   for (k=1; k<=2; k++) {     */
     for (i=1;i<=npar;i++) p2[i]=x[i];  }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*************************free matrix ************************/
     k1=func(p2)-fx;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
    {
     p2[thetai]=x[thetai]+delti[thetai]/k;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    free((FREE_ARG)(m+nrl-NR_END));
     k2=func(p2)-fx;  }
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /******************* ma3x *******************************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     k3=func(p2)-fx;  {
      long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     p2[thetai]=x[thetai]-delti[thetai]/k;    double ***m;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    if (!m) nrerror("allocation failure 1 in matrix()");
 #ifdef DEBUG    m += NR_END;
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    m -= nrl;
 #endif  
   }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   return res;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 {  
   int i,imax,j,k;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double big,dum,sum,temp;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double *vv;    m[nrl][ncl] += NR_END;
      m[nrl][ncl] -= nll;
   vv=vector(1,n);    for (j=ncl+1; j<=nch; j++) 
   *d=1.0;      m[nrl][j]=m[nrl][j-1]+nlay;
   for (i=1;i<=n;i++) {    
     big=0.0;    for (i=nrl+1; i<=nrh; i++) {
     for (j=1;j<=n;j++)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       if ((temp=fabs(a[i][j])) > big) big=temp;      for (j=ncl+1; j<=nch; j++) 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        m[i][j]=m[i][j-1]+nlay;
     vv[i]=1.0/big;    }
   }    return m; 
   for (j=1;j<=n;j++) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for (i=1;i<j;i++) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       sum=a[i][j];    */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  }
       a[i][j]=sum;  
     }  /*************************free ma3x ************************/
     big=0.0;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     for (i=j;i<=n;i++) {  {
       sum=a[i][j];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       for (k=1;k<j;k++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         sum -= a[i][k]*a[k][j];    free((FREE_ARG)(m+nrl-NR_END));
       a[i][j]=sum;  }
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  /*************** function subdirf ***********/
         imax=i;  char *subdirf(char fileres[])
       }  {
     }    /* Caution optionfilefiname is hidden */
     if (j != imax) {    strcpy(tmpout,optionfilefiname);
       for (k=1;k<=n;k++) {    strcat(tmpout,"/"); /* Add to the right */
         dum=a[imax][k];    strcat(tmpout,fileres);
         a[imax][k]=a[j][k];    return tmpout;
         a[j][k]=dum;  }
       }  
       *d = -(*d);  /*************** function subdirf2 ***********/
       vv[imax]=vv[j];  char *subdirf2(char fileres[], char *preop)
     }  {
     indx[j]=imax;    
     if (a[j][j] == 0.0) a[j][j]=TINY;    /* Caution optionfilefiname is hidden */
     if (j != n) {    strcpy(tmpout,optionfilefiname);
       dum=1.0/(a[j][j]);    strcat(tmpout,"/");
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    strcat(tmpout,preop);
     }    strcat(tmpout,fileres);
   }    return tmpout;
   free_vector(vv,1,n);  /* Doesn't work */  }
 ;  
 }  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
 void lubksb(double **a, int n, int *indx, double b[])  {
 {    
   int i,ii=0,ip,j;    /* Caution optionfilefiname is hidden */
   double sum;    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/");
   for (i=1;i<=n;i++) {    strcat(tmpout,preop);
     ip=indx[i];    strcat(tmpout,preop2);
     sum=b[ip];    strcat(tmpout,fileres);
     b[ip]=b[i];    return tmpout;
     if (ii)  }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  char *asc_diff_time(long time_sec, char ascdiff[])
     b[i]=sum;  {
   }    long sec_left, days, hours, minutes;
   for (i=n;i>=1;i--) {    days = (time_sec) / (60*60*24);
     sum=b[i];    sec_left = (time_sec) % (60*60*24);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    hours = (sec_left) / (60*60) ;
     b[i]=sum/a[i][i];    sec_left = (sec_left) %(60*60);
   }    minutes = (sec_left) /60;
 }    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
 /************ Frequencies ********************/    return ascdiff;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  }
 {  /* Some frequencies */  
    /***************** f1dim *************************/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  extern int ncom; 
   double ***freq; /* Frequencies */  extern double *pcom,*xicom;
   double *pp;  extern double (*nrfunc)(double []); 
   double pos, k2, dateintsum=0,k2cpt=0;   
   FILE *ficresp;  double f1dim(double x) 
   char fileresp[FILENAMELENGTH];  { 
      int j; 
   pp=vector(1,nlstate);    double f;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    double *xt; 
   strcpy(fileresp,"p");   
   strcat(fileresp,fileres);    xt=vector(1,ncom); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    f=(*nrfunc)(xt); 
     exit(0);    free_vector(xt,1,ncom); 
   }    return f; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  } 
   j1=0;  
    /*****************brent *************************/
   j=cptcoveff;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  { 
      int iter; 
   for(k1=1; k1<=j;k1++){    double a,b,d,etemp;
     for(i1=1; i1<=ncodemax[k1];i1++){    double fu=0,fv,fw,fx;
       j1++;    double ftemp=0.;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         scanf("%d", i);*/    double e=0.0; 
       for (i=-1; i<=nlstate+ndeath; i++)     
         for (jk=-1; jk<=nlstate+ndeath; jk++)      a=(ax < cx ? ax : cx); 
           for(m=agemin; m <= agemax+3; m++)    b=(ax > cx ? ax : cx); 
             freq[i][jk][m]=0;    x=w=v=bx; 
          fw=fv=fx=(*f)(x); 
       dateintsum=0;    for (iter=1;iter<=ITMAX;iter++) { 
       k2cpt=0;      xm=0.5*(a+b); 
       for (i=1; i<=imx; i++) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         bool=1;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         if  (cptcovn>0) {      printf(".");fflush(stdout);
           for (z1=1; z1<=cptcoveff; z1++)      fprintf(ficlog,".");fflush(ficlog);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  #ifdef DEBUGBRENT
               bool=0;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         if (bool==1) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
           for(m=firstpass; m<=lastpass; m++){  #endif
             k2=anint[m][i]+(mint[m][i]/12.);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        *xmin=x; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;        return fx; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      } 
               if (m<lastpass) {      ftemp=fu;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      if (fabs(e) > tol1) { 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        r=(x-w)*(fx-fv); 
               }        q=(x-v)*(fx-fw); 
                      p=(x-v)*q-(x-w)*r; 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        q=2.0*(q-r); 
                 dateintsum=dateintsum+k2;        if (q > 0.0) p = -p; 
                 k2cpt++;        q=fabs(q); 
               }        etemp=e; 
             }        e=d; 
           }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }        else { 
                  d=p/q; 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
       if  (cptcovn>0) {            d=SIGN(tol1,xm-x); 
         fprintf(ficresp, "\n#********** Variable ");        } 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } else { 
         fprintf(ficresp, "**********\n#");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }      } 
       for(i=1; i<=nlstate;i++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      fu=(*f)(u); 
       fprintf(ficresp, "\n");      if (fu <= fx) { 
              if (u >= x) a=x; else b=x; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){        SHFT(v,w,x,u) 
         if(i==(int)agemax+3)          SHFT(fv,fw,fx,fu) 
           printf("Total");          } else { 
         else            if (u < x) a=u; else b=u; 
           printf("Age %d", i);            if (fu <= fw || w == x) { 
         for(jk=1; jk <=nlstate ; jk++){              v=w; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              w=u; 
             pp[jk] += freq[jk][m][i];              fv=fw; 
         }              fw=fu; 
         for(jk=1; jk <=nlstate ; jk++){            } else if (fu <= fv || v == x || v == w) { 
           for(m=-1, pos=0; m <=0 ; m++)              v=u; 
             pos += freq[jk][m][i];              fv=fu; 
           if(pp[jk]>=1.e-10)            } 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          } 
           else    } 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    nrerror("Too many iterations in brent"); 
         }    *xmin=x; 
     return fx; 
         for(jk=1; jk <=nlstate ; jk++){  } 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];  /****************** mnbrak ***********************/
         }  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         for(jk=1,pos=0; jk <=nlstate ; jk++)              double (*func)(double)) 
           pos += pp[jk];  { 
         for(jk=1; jk <=nlstate ; jk++){    double ulim,u,r,q, dum;
           if(pos>=1.e-5)    double fu; 
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);   
           else    *fa=(*func)(*ax); 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    *fb=(*func)(*bx); 
           if( i <= (int) agemax){    if (*fb > *fa) { 
             if(pos>=1.e-5){      SHFT(dum,*ax,*bx,dum) 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        SHFT(dum,*fb,*fa,dum) 
               probs[i][jk][j1]= pp[jk]/pos;        } 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    *cx=(*bx)+GOLD*(*bx-*ax); 
             }    *fc=(*func)(*cx); 
             else    while (*fb > *fc) { /* Declining fa, fb, fc */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      r=(*bx-*ax)*(*fb-*fc); 
           }      q=(*bx-*cx)*(*fb-*fa); 
         }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
                (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
         for(jk=-1; jk <=nlstate+ndeath; jk++)      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
           for(m=-1; m <=nlstate+ndeath; m++)      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        fu=(*func)(u); 
         if(i <= (int) agemax)  #ifdef DEBUG
           fprintf(ficresp,"\n");        /* f(x)=A(x-u)**2+f(u) */
         printf("\n");        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);
   dateintmean=dateintsum/k2cpt;        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);
    #endif 
   fclose(ficresp);      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        fu=(*func)(u); 
   free_vector(pp,1,nlstate);        if (fu < *fc) { 
            SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   /* End of Freq */            SHFT(*fb,*fc,fu,(*func)(u)) 
 }            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
 /************ Prevalence ********************/        u=ulim; 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        fu=(*func)(u); 
 {  /* Some frequencies */      } else { 
          u=(*cx)+GOLD*(*cx-*bx); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        fu=(*func)(u); 
   double ***freq; /* Frequencies */      } 
   double *pp;      SHFT(*ax,*bx,*cx,u) 
   double pos, k2;        SHFT(*fa,*fb,*fc,fu) 
         } 
   pp=vector(1,nlstate);  } 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
    /*************** linmin ************************/
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
   j1=0;  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
    and replaces xi by the actual vector displacement that p was moved. Also returns as fret
   j=cptcoveff;  the value of func at the returned location p . This is actually all accomplished by calling the
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  routines mnbrak and brent .*/
    int ncom; 
   for(k1=1; k1<=j;k1++){  double *pcom,*xicom;
     for(i1=1; i1<=ncodemax[k1];i1++){  double (*nrfunc)(double []); 
       j1++;   
        void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       for (i=-1; i<=nlstate+ndeath; i++)    { 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double brent(double ax, double bx, double cx, 
           for(m=agemin; m <= agemax+3; m++)                 double (*f)(double), double tol, double *xmin); 
             freq[i][jk][m]=0;    double f1dim(double x); 
          void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       for (i=1; i<=imx; i++) {                double *fc, double (*func)(double)); 
         bool=1;    int j; 
         if  (cptcovn>0) {    double xx,xmin,bx,ax; 
           for (z1=1; z1<=cptcoveff; z1++)    double fx,fb,fa;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])   
               bool=0;    ncom=n; 
         }    pcom=vector(1,n); 
         if (bool==1) {    xicom=vector(1,n); 
           for(m=firstpass; m<=lastpass; m++){    nrfunc=func; 
             k2=anint[m][i]+(mint[m][i]/12.);    for (j=1;j<=n;j++) { 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      pcom[j]=p[j]; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      xicom[j]=xi[j]; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    } 
               if (m<lastpass) {    ax=0.0; 
                 if (calagedate>0)    xx=1.0; 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
                 else    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  #ifdef DEBUG
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
               }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
             }  #endif
           }    for (j=1;j<=n;j++) { 
         }      xi[j] *= xmin; 
       }      p[j] += xi[j]; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){    } 
         for(jk=1; jk <=nlstate ; jk++){    free_vector(xicom,1,n); 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    free_vector(pcom,1,n); 
             pp[jk] += freq[jk][m][i];  } 
         }  
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  /*************** powell ************************/
             pos += freq[jk][m][i];  /*
         }  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-
         for(jk=1; jk <=nlstate ; jk++){  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  such that failure to decrease by more than this amount on one iteration signals doneness. On
             pp[jk] += freq[jk][m][i];  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(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                      double (*func)(double [])) 
         for(jk=1; jk <=nlstate ; jk++){      { 
           if( i <= (int) agemax){    void linmin(double p[], double xi[], int n, double *fret, 
             if(pos>=1.e-5){                double (*func)(double [])); 
               probs[i][jk][j1]= pp[jk]/pos;    int i,ibig,j; 
             }    double del,t,*pt,*ptt,*xit;
           }    double fp,fptt;
         }    double *xits;
            int niterf, itmp;
       }  
     }    pt=vector(1,n); 
   }    ptt=vector(1,n); 
     xit=vector(1,n); 
      xits=vector(1,n); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    *fret=(*func)(p); 
   free_vector(pp,1,nlstate);    for (j=1;j<=n;j++) pt[j]=p[j]; 
        rcurr_time = time(NULL);  
 }  /* End of Freq */    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 /************* Waves Concatenation ***************/      ibig=0; 
       del=0.0; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      rlast_time=rcurr_time;
 {      /* (void) gettimeofday(&curr_time,&tzp); */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      rcurr_time = time(NULL);  
      Death is a valid wave (if date is known).      curr_time = *localtime(&rcurr_time);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
      and mw[mi+1][i]. dh depends on stepm.  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
      */     for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
   int i, mi, m;        fprintf(ficlog," %d %.12lf",i, p[i]);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        fprintf(ficrespow," %.12lf", p[i]);
      double sum=0., jmean=0.;*/      }
       printf("\n");
   int j, k=0,jk, ju, jl;      fprintf(ficlog,"\n");
   double sum=0.;      fprintf(ficrespow,"\n");fflush(ficrespow);
   jmin=1e+5;      if(*iter <=3){
   jmax=-1;        tml = *localtime(&rcurr_time);
   jmean=0.;        strcpy(strcurr,asctime(&tml));
   for(i=1; i<=imx; i++){        rforecast_time=rcurr_time; 
     mi=0;        itmp = strlen(strcurr);
     m=firstpass;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     while(s[m][i] <= nlstate){          strcurr[itmp-1]='\0';
       if(s[m][i]>=1)        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         mw[++mi][i]=m;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       if(m >=lastpass)        for(niterf=10;niterf<=30;niterf+=10){
         break;          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
       else          forecast_time = *localtime(&rforecast_time);
         m++;          strcpy(strfor,asctime(&forecast_time));
     }/* end while */          itmp = strlen(strfor);
     if (s[m][i] > nlstate){          if(strfor[itmp-1]=='\n')
       mi++;     /* Death is another wave */          strfor[itmp-1]='\0';
       /* if(mi==0)  never been interviewed correctly before death */          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);
          /* Only death is a correct wave */          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);
       mw[mi][i]=m;        }
     }      }
       for (i=1;i<=n;i++) { 
     wav[i]=mi;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     if(mi==0)        fptt=(*fret); 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  #ifdef DEBUG
   }            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
             fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   for(i=1; i<=imx; i++){  #endif
     for(mi=1; mi<wav[i];mi++){        printf("%d",i);fflush(stdout);
       if (stepm <=0)        fprintf(ficlog,"%d",i);fflush(ficlog);
         dh[mi][i]=1;        linmin(p,xit,n,fret,func); 
       else{        if (fabs(fptt-(*fret)) > del) { 
         if (s[mw[mi+1][i]][i] > nlstate) {          del=fabs(fptt-(*fret)); 
           if (agedc[i] < 2*AGESUP) {          ibig=i; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        } 
           if(j==0) j=1;  /* Survives at least one month after exam */  #ifdef DEBUG
           k=k+1;        printf("%d %.12e",i,(*fret));
           if (j >= jmax) jmax=j;        fprintf(ficlog,"%d %.12e",i,(*fret));
           if (j <= jmin) jmin=j;        for (j=1;j<=n;j++) {
           sum=sum+j;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          printf(" x(%d)=%.12e",j,xit[j]);
           }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }        }
         else{        for(j=1;j<=n;j++) {
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          printf(" p(%d)=%.12e",j,p[j]);
           k=k+1;          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
           if (j >= jmax) jmax=j;        }
           else if (j <= jmin)jmin=j;        printf("\n");
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        fprintf(ficlog,"\n");
           sum=sum+j;  #endif
         }      } /* end i */
         jk= j/stepm;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         jl= j -jk*stepm;  #ifdef DEBUG
         ju= j -(jk+1)*stepm;        int k[2],l;
         if(jl <= -ju)        k[0]=1;
           dh[mi][i]=jk;        k[1]=-1;
         else        printf("Max: %.12e",(*func)(p));
           dh[mi][i]=jk+1;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         if(dh[mi][i]==0)        for (j=1;j<=n;j++) {
           dh[mi][i]=1; /* At least one step */          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
     }        }
   }        printf("\n");
   jmean=sum/k;        fprintf(ficlog,"\n");
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        for(l=0;l<=1;l++) {
  }          for (j=1;j<=n;j++) {
 /*********** Tricode ****************************/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 void tricode(int *Tvar, int **nbcode, int imx)            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]);
   int Ndum[20],ij=1, k, j, i;          }
   int cptcode=0;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   cptcoveff=0;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
          }
   for (k=0; k<19; k++) Ndum[k]=0;  #endif
   for (k=1; k<=7; k++) ncodemax[k]=0;  
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        free_vector(xit,1,n); 
     for (i=1; i<=imx; i++) {        free_vector(xits,1,n); 
       ij=(int)(covar[Tvar[j]][i]);        free_vector(ptt,1,n); 
       Ndum[ij]++;        free_vector(pt,1,n); 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        return; 
       if (ij > cptcode) cptcode=ij;      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { /* Computes an extrapolated point */
     for (i=0; i<=cptcode; i++) {        ptt[j]=2.0*p[j]-pt[j]; 
       if(Ndum[i]!=0) ncodemax[j]++;        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
     ij=1;      } 
       fptt=(*func)(ptt); 
       if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
     for (i=1; i<=ncodemax[j]; i++) {        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       for (k=0; k<=19; k++) {        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         if (Ndum[k] != 0) {        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
           nbcode[Tvar[j]][ij]=k;        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
                  /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
           ij++;        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
         }        /* Thus we compare delta(2h) with observed f1-f3 */
         if (ij > ncodemax[j]) break;        /* or best gain on one ancient line 'del' with total  */
       }          /* gain f1-f2 = f1 - f2 - 'del' with del  */
     }        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   }    
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
  for (k=0; k<19; k++) Ndum[k]=0;        t= t- del*SQR(fp-fptt);
         printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
  for (i=1; i<=ncovmodel-2; i++) {        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
       ij=Tvar[i];  #ifdef DEBUG
       Ndum[ij]++;        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),
  ij=1;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
  for (i=1; i<=10; i++) {        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
    if((Ndum[i]!=0) && (i<=ncovcol)){        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);
      Tvaraff[ij]=i;  #endif
      ij++;        if (t < 0.0) { /* Then we use it for last direction */
    }          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
  }          for (j=1;j<=n;j++) { 
              xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
     cptcoveff=ij-1;            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
 }          }
           printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
 /*********** Health Expectancies ****************/          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )  #ifdef DEBUG
           printf("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);
   /* Health expectancies */          for(j=1;j<=n;j++){
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;            printf(" %.12e",xit[j]);
   double age, agelim, hf;            fprintf(ficlog," %.12e",xit[j]);
   double ***p3mat,***varhe;          }
   double **dnewm,**doldm;          printf("\n");
   double *xp;          fprintf(ficlog,"\n");
   double **gp, **gm;  #endif
   double ***gradg, ***trgradg;        } /* end of t negative */
   int theta;      } /* end if (fptt < fp)  */
     } 
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);  } 
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate*2,1,npar);  /**** Prevalence limit (stable or period prevalence)  ****************/
   doldm=matrix(1,nlstate*2,1,nlstate*2);  
    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   fprintf(ficreseij,"# Health expectancies\n");  {
   fprintf(ficreseij,"# Age");    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for(i=1; i<=nlstate;i++)       matrix by transitions matrix until convergence is reached */
     for(j=1; j<=nlstate;j++)    
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    int i, ii,j,k;
   fprintf(ficreseij,"\n");    double min, max, maxmin, maxmax,sumnew=0.;
     /* double **matprod2(); */ /* test */
   if(estepm < stepm){    double **out, cov[NCOVMAX+1], **pmij();
     printf ("Problem %d lower than %d\n",estepm, stepm);    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
   else  hstepm=estepm;      
   /* We compute the life expectancy from trapezoids spaced every estepm months    for (ii=1;ii<=nlstate+ndeath;ii++)
    * This is mainly to measure the difference between two models: for example      for (j=1;j<=nlstate+ndeath;j++){
    * if stepm=24 months pijx are given only every 2 years and by summing them        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    * we are calculating an estimate of the Life Expectancy assuming a linear      }
    * progression inbetween and thus overestimating or underestimating according    
    * to the curvature of the survival function. If, for the same date, we    cov[1]=1.;
    * 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    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
    * hypothesis. A more precise result, taking into account a more precise    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
    * curvature will be obtained if estepm is as small as stepm. */      newm=savm;
       /* Covariates have to be included here again */
   /* For example we decided to compute the life expectancy with the smallest unit */      cov[2]=agefin;
   /* 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      for (k=1; k<=cptcovn;k++) {
      nstepm is the number of stepm from age to agelin.        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      Look at hpijx to understand the reason of that which relies in memory size        /*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]]);*/
      and note for a fixed period like estepm months */      }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
      survival function given by stepm (the optimization length). Unfortunately it      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
      means that if the survival funtion is printed only each two years of age and if      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
      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.      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   */      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   agelim=AGESUP;      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
     /* nhstepm age range expressed in number of stepm */      
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      savm=oldm;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      oldm=newm;
     /* if (stepm >= YEARM) hstepm=1;*/      maxmax=0.;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for(j=1;j<=nlstate;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        min=1.;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        max=0.;
     gp=matrix(0,nhstepm,1,nlstate*2);        for(i=1; i<=nlstate; i++) {
     gm=matrix(0,nhstepm,1,nlstate*2);          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          prlim[i][j]= newm[i][j]/(1-sumnew);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            max=FMAX(max,prlim[i][j]);
            min=FMIN(min,prlim[i][j]);
         }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
     /* Computing Variances of health expectancies */      } /* j loop */
       if(maxmax < ftolpl){
      for(theta=1; theta <=npar; theta++){        return prlim;
       for(i=1; i<=npar; i++){      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    } /* age loop */
       }    return prlim; /* should not reach here */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    }
    
       cptj=0;  /*************** transition probabilities ***************/ 
       for(j=1; j<= nlstate; j++){  
         for(i=1; i<=nlstate; i++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
           cptj=cptj+1;  {
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    /* According to parameters values stored in x and the covariate's values stored in cov,
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;       computes the probability to be observed in state j being in state i by appying the
           }       model to the ncovmodel covariates (including constant and age).
         }       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
       }       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
             ncth covariate in the global vector x is given by the formula:
             j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
       for(i=1; i<=npar; i++)       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
             Outputs ps[i][j] the probability to be observed in j being in j according to
       cptj=0;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
       for(j=1; j<= nlstate; j++){    */
         for(i=1;i<=nlstate;i++){    double s1, lnpijopii;
           cptj=cptj+1;    /*double t34;*/
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    int i,j, nc, ii, jj;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }      for(i=1; i<= nlstate; i++){
         }        for(j=1; j<i;j++){
       }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       for(j=1; j<= nlstate*2; j++)            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         for(h=0; h<=nhstepm-1; h++){            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }          }
      }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
      /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
 /* End theta */        }
         for(j=i+1; j<=nlstate+ndeath;j++){
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
      for(h=0; h<=nhstepm-1; h++)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       for(j=1; j<=nlstate*2;j++)  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         for(theta=1; theta <=npar; theta++)          }
           trgradg[h][j][theta]=gradg[h][theta][j];          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
              }
       }
      for(i=1;i<=nlstate*2;i++)      
       for(j=1;j<=nlstate*2;j++)      for(i=1; i<= nlstate; i++){
         varhe[i][j][(int)age] =0.;        s1=0;
         for(j=1; j<i; j++){
      printf("%d|",(int)age);fflush(stdout);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
      for(h=0;h<=nhstepm-1;h++){          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       for(k=0;k<=nhstepm-1;k++){        }
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        for(j=i+1; j<=nlstate+ndeath; j++){
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         for(i=1;i<=nlstate*2;i++)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           for(j=1;j<=nlstate*2;j++)        }
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       }        ps[i][i]=1./(s1+1.);
     }        /* Computing other pijs */
     /* Computing expectancies */        for(j=1; j<i; j++)
     for(i=1; i<=nlstate;i++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=1; j<=nlstate;j++)        for(j=i+1; j<=nlstate+ndeath; j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          ps[i][j]= exp(ps[i][j])*ps[i][i];
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                } /* end i */
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         }        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
     fprintf(ficreseij,"%3.0f",age );          ps[ii][ii]=1;
     cptj=0;        }
     for(i=1; i<=nlstate;i++)      }
       for(j=1; j<=nlstate;j++){      
         cptj++;      
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       }      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     fprintf(ficreseij,"\n");      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
          /*   } */
     free_matrix(gm,0,nhstepm,1,nlstate*2);      /*   printf("\n "); */
     free_matrix(gp,0,nhstepm,1,nlstate*2);      /* } */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      /* printf("\n ");printf("%lf ",cov[2]);*/
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      /*
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   }        goto end;*/
   printf("\n");      return ps;
   }
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);  /**************** Product of 2 matrices ******************/
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
 }  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
 /************ Variance ******************/       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    /* in, b, out are matrice of pointers which should have been initialized 
 {       before: only the contents of out is modified. The function returns
   /* Variance of health expectancies */       a pointer to pointers identical to out */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int i, j, k;
   double **newm;    for(i=nrl; i<= nrh; i++)
   double **dnewm,**doldm;      for(k=ncolol; k<=ncoloh; k++){
   int i, j, nhstepm, hstepm, h, nstepm ;        out[i][k]=0.;
   int k, cptcode;        for(j=ncl; j<=nch; j++)
   double *xp;          out[i][k] +=in[i][j]*b[j][k];
   double **gp, **gm;      }
   double ***gradg, ***trgradg;    return out;
   double ***p3mat;  }
   double age,agelim, hf;  
   int theta;  
   /************* Higher Matrix Product ***************/
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");  
   fprintf(ficresvij,"# Age");  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   for(i=1; i<=nlstate;i++)  {
     for(j=1; j<=nlstate;j++)    /* Computes the transition matrix starting at age 'age' over 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);       'nhstepm*hstepm*stepm' months (i.e. until
   fprintf(ficresvij,"\n");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
   xp=vector(1,npar);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   dnewm=matrix(1,nlstate,1,npar);       (typically every 2 years instead of every month which is too big 
   doldm=matrix(1,nlstate,1,nlstate);       for the memory).
         Model is determined by parameters x and covariates have to be 
   if(estepm < stepm){       included manually here. 
     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 */    int i, j, d, h, k;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double **out, cov[NCOVMAX+1];
      nhstepm is the number of hstepm from age to agelim    double **newm;
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size    /* Hstepm could be zero and should return the unit matrix */
      and note for a fixed period like k years */    for (i=1;i<=nlstate+ndeath;i++)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      for (j=1;j<=nlstate+ndeath;j++){
      survival function given by stepm (the optimization length). Unfortunately it        oldm[i][j]=(i==j ? 1.0 : 0.0);
      means that if the survival funtion is printed only each two years of age and if        po[i][j][0]=(i==j ? 1.0 : 0.0);
      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.    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   */    for(h=1; h <=nhstepm; h++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      for(d=1; d <=hstepm; d++){
   agelim = AGESUP;        newm=savm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        /* Covariates have to be included here again */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        cov[1]=1.;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovn;k++) 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     gp=matrix(0,nhstepm,1,nlstate);        for (k=1; k<=cptcovage;k++)
     gm=matrix(0,nhstepm,1,nlstate);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
     for(theta=1; theta <=npar; theta++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
       if (popbased==1) {        savm=oldm;
         for(i=1; i<=nlstate;i++)        oldm=newm;
           prlim[i][i]=probs[(int)age][i][ij];      }
       }      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
       for(j=1; j<= nlstate; j++){          po[i][j][h]=newm[i][j];
         for(h=0; h<=nhstepm; h++){          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      /*printf("h=%d ",h);*/
         }    } /* end h */
       }  /*     printf("\n H=%d \n",h); */
        return po;
       for(i=1; i<=npar; i++) /* Computes gradient */  }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #ifdef NLOPT
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
      double fret;
       if (popbased==1) {    double *xt;
         for(i=1; i<=nlstate;i++)    int j;
           prlim[i][i]=probs[(int)age][i][ij];    myfunc_data *d2 = (myfunc_data *) pd;
       }  /* xt = (p1-1); */
     xt=vector(1,n); 
       for(j=1; j<= nlstate; j++){    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
         }    printf("Function = %.12lf ",fret);
       }    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf("\n");
       for(j=1; j<= nlstate; j++)   free_vector(xt,1,n);
         for(h=0; h<=nhstepm; h++){    return fret;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  }
         }  #endif
     } /* End theta */  
   /*************** log-likelihood *************/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  double func( double *x)
   {
     for(h=0; h<=nhstepm; h++)    int i, ii, j, k, mi, d, kk;
       for(j=1; j<=nlstate;j++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         for(theta=1; theta <=npar; theta++)    double **out;
           trgradg[h][j][theta]=gradg[h][theta][j];    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    int s1, s2;
     for(i=1;i<=nlstate;i++)    double bbh, survp;
       for(j=1;j<=nlstate;j++)    long ipmx;
         vareij[i][j][(int)age] =0.;    /*extern weight */
     /* We are differentiating ll according to initial status */
     for(h=0;h<=nhstepm;h++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for(k=0;k<=nhstepm;k++){    /*for(i=1;i<imx;i++) 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      printf(" %d\n",s[4][i]);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    */
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)    ++countcallfunc;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }    cov[1]=1.;
     }  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    if(mle==1){
       for(j=1; j<=nlstate;j++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        /* 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(ficresvij,"\n");           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
     free_matrix(gp,0,nhstepm,1,nlstate);           to be observed in j being in i according to the model.
     free_matrix(gm,0,nhstepm,1,nlstate);         */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          cov[2+k]=covar[Tvar[k]][i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
   } /* End age */        /* 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] 
   free_vector(xp,1,npar);           has been calculated etc */
   free_matrix(doldm,1,nlstate,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   free_matrix(dnewm,1,nlstate,1,nlstate);          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);
 /************ 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(d=0; d<dh[mi][i]; d++){
 {            newm=savm;
   /* Variance of prevalence limit */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for (kk=1; kk<=cptcovage;kk++) {
   double **newm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
   double **dnewm,**doldm;            }
   int i, j, nhstepm, hstepm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int k, cptcode;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double *xp;            savm=oldm;
   double *gp, *gm;            oldm=newm;
   double **gradg, **trgradg;          } /* end mult */
   double age,agelim;        
   int theta;          /*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.
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   fprintf(ficresvpl,"# Age");           * (in months) between two waves is not a multiple of stepm, we rounded to 
   for(i=1; i<=nlstate;i++)           * the nearest (and in case of equal distance, to the lowest) interval but now
       fprintf(ficresvpl," %1d-%1d",i,i);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   fprintf(ficresvpl,"\n");           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
   xp=vector(1,npar);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   dnewm=matrix(1,nlstate,1,npar);           * -stepm/2 to stepm/2 .
   doldm=matrix(1,nlstate,1,nlstate);           * For stepm=1 the results are the same as for previous versions of Imach.
             * For stepm > 1 the results are less biased than in previous versions. 
   hstepm=1*YEARM; /* Every year of age */           */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          s1=s[mw[mi][i]][i];
   agelim = AGESUP;          s2=s[mw[mi+1][i]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          bbh=(double)bh[mi][i]/(double)stepm; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          /* bias bh is positive if real duration
     if (stepm >= YEARM) hstepm=1;           * is higher than the multiple of stepm and negative otherwise.
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */           */
     gradg=matrix(1,npar,1,nlstate);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     gp=vector(1,nlstate);          if( s2 > nlstate){ 
     gm=vector(1,nlstate);            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
     for(theta=1; theta <=npar; theta++){               die between last step unit time and current  step unit time, 
       for(i=1; i<=npar; i++){ /* Computes gradient */               which is also equal to probability to die before dh 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);               minus probability to die before dh-stepm . 
       }               In version up to 0.92 likelihood was computed
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          as if date of death was unknown. Death was treated as any other
       for(i=1;i<=nlstate;i++)          health state: the date of the interview describes the actual state
         gp[i] = prlim[i][i];          and not the date of a change in health state. The former idea was
              to consider that at each interview the state was recorded
       for(i=1; i<=npar; i++) /* Computes gradient */          (healthy, disable or death) and IMaCh was corrected; but when we
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          introduced the exact date of death then we should have modified
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          the contribution of an exact death to the likelihood. This new
       for(i=1;i<=nlstate;i++)          contribution is smaller and very dependent of the step unit
         gm[i] = prlim[i][i];          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
       for(i=1;i<=nlstate;i++)          interview up to one month before death multiplied by the
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          probability to die within a month. Thanks to Chris
     } /* End theta */          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
     trgradg =matrix(1,nlstate,1,npar);          which slows down the processing. The difference can be up to 10%
           lower mortality.
     for(j=1; j<=nlstate;j++)            */
       for(theta=1; theta <=npar; theta++)            lli=log(out[s1][s2] - savm[s1][s2]);
         trgradg[j][theta]=gradg[theta][j];  
   
     for(i=1;i<=nlstate;i++)          } else if  (s2==-2) {
       varpl[i][(int)age] =0.;            for (j=1,survp=0. ; j<=nlstate; j++) 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            /*survp += out[s1][j]; */
     for(i=1;i<=nlstate;i++)            lli= log(survp);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          }
           
     fprintf(ficresvpl,"%.0f ",age );          else if  (s2==-4) { 
     for(i=1; i<=nlstate;i++)            for (j=3,survp=0. ; j<=nlstate; j++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     fprintf(ficresvpl,"\n");            lli= log(survp); 
     free_vector(gp,1,nlstate);          } 
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);          else if  (s2==-5) { 
     free_matrix(trgradg,1,nlstate,1,npar);            for (j=1,survp=0. ; j<=2; j++)  
   } /* End age */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
   free_vector(xp,1,npar);          } 
   free_matrix(doldm,1,nlstate,1,npar);          
   free_matrix(dnewm,1,nlstate,1,nlstate);          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
 /************ Variance of one-step probabilities  ******************/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          /*if(lli ==000.0)*/
 {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int i, j,  i1, k1, l1;          ipmx +=1;
   int k2, l2, j1,  z1;          sw += weight[i];
   int k=0,l, cptcode;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int first=1;        } /* end of wave */
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;      } /* end of individual */
   double **dnewm,**doldm;    }  else if(mle==2){
   double *xp;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double *gp, *gm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **gradg, **trgradg;        for(mi=1; mi<= wav[i]-1; mi++){
   double **mu;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double age,agelim, cov[NCOVMAX];            for (j=1;j<=nlstate+ndeath;j++){
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int theta;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   char fileresprob[FILENAMELENGTH];            }
   char fileresprobcov[FILENAMELENGTH];          for(d=0; d<=dh[mi][i]; d++){
   char fileresprobcor[FILENAMELENGTH];            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***varpij;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   strcpy(fileresprob,"prob");            }
   strcat(fileresprob,fileres);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf("Problem with resultfile: %s\n", fileresprob);            savm=oldm;
   }            oldm=newm;
   strcpy(fileresprobcov,"probcov");          } /* end mult */
   strcat(fileresprobcov,fileres);        
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {          s1=s[mw[mi][i]][i];
     printf("Problem with resultfile: %s\n", fileresprobcov);          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
   strcpy(fileresprobcor,"probcor");          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 */
   strcat(fileresprobcor,fileres);          ipmx +=1;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {          sw += weight[i];
     printf("Problem with resultfile: %s\n", fileresprobcor);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      } /* end of individual */
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    }  else if(mle==3){  /* exponential inter-extrapolation */
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");        for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficresprob,"# Age");          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");            for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficresprobcov,"# Age");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresprobcov,"# Age");            }
           for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   for(i=1; i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(j=1; j<=(nlstate+ndeath);j++){            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       fprintf(ficresprobcov," p%1d-%1d ",i,j);            }
       fprintf(ficresprobcor," p%1d-%1d ",i,j);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficresprob,"\n");            savm=oldm;
   fprintf(ficresprobcov,"\n");            oldm=newm;
   fprintf(ficresprobcor,"\n");          } /* end mult */
   xp=vector(1,npar);        
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          s1=s[mw[mi][i]][i];
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));          s2=s[mw[mi+1][i]][i];
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);          bbh=(double)bh[mi][i]/(double)stepm; 
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);          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 */
   first=1;          ipmx +=1;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          sw += weight[i];
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     exit(0);        } /* end of wave */
   }      } /* end of individual */
   else{    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     fprintf(ficgp,"\n# Routine varprob");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        for(mi=1; mi<= wav[i]-1; mi++){
     printf("Problem with html file: %s\n", optionfilehtm);          for (ii=1;ii<=nlstate+ndeath;ii++)
     exit(0);            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   else{              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");            }
     fprintf(fichtm,"\n<br> We have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");          for(d=0; d<dh[mi][i]; d++){
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
   cov[1]=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   j=cptcoveff;            }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          
   j1=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(k1=1; k1<=1;k1++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i1=1; i1<=ncodemax[k1];i1++){            savm=oldm;
     j1++;            oldm=newm;
           } /* end mult */
     if  (cptcovn>0) {        
       fprintf(ficresprob, "\n#********** Variable ");          s1=s[mw[mi][i]][i];
       fprintf(ficresprobcov, "\n#********** Variable ");          s2=s[mw[mi+1][i]][i];
       fprintf(ficgp, "\n#********** Variable ");          if( s2 > nlstate){ 
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");            lli=log(out[s1][s2] - savm[s1][s2]);
       fprintf(ficresprobcor, "\n#********** Variable ");          }else{
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficresprob, "**********\n#");          }
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          ipmx +=1;
       fprintf(ficresprobcov, "**********\n#");          sw += weight[i];
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficgp, "**********\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]); */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        } /* end of wave */
       fprintf(ficgp, "**********\n#");      } /* end of individual */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       fprintf(fichtm, "**********\n#");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
            for(mi=1; mi<= wav[i]-1; mi++){
       for (age=bage; age<=fage; age ++){          for (ii=1;ii<=nlstate+ndeath;ii++)
         cov[2]=age;            for (j=1;j<=nlstate+ndeath;j++){
         for (k=1; k<=cptcovn;k++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          for(d=0; d<dh[mi][i]; d++){
         for (k=1; k<=cptcovprod;k++)            newm=savm;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                    for (kk=1; kk<=cptcovage;kk++) {
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);            }
         gp=vector(1,(nlstate)*(nlstate+ndeath));          
         gm=vector(1,(nlstate)*(nlstate+ndeath));            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(theta=1; theta <=npar; theta++){            savm=oldm;
           for(i=1; i<=npar; i++)            oldm=newm;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          } /* end mult */
                  
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          s1=s[mw[mi][i]][i];
                    s2=s[mw[mi+1][i]][i];
           k=0;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           for(i=1; i<= (nlstate); i++){          ipmx +=1;
             for(j=1; j<=(nlstate+ndeath);j++){          sw += weight[i];
               k=k+1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               gp[k]=pmmij[i][j];          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
             }        } /* end of wave */
           }      } /* end of individual */
              } /* End of if */
           for(i=1; i<=npar; i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    /* 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 */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    return -l;
           k=0;  }
           for(i=1; i<=(nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){  /*************** log-likelihood *************/
               k=k+1;  double funcone( double *x)
               gm[k]=pmmij[i][j];  {
             }    /* Same as likeli but slower because of a lot of printf and if */
           }    int i, ii, j, k, mi, d, kk;
          double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    double **out;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      double lli; /* Individual log likelihood */
         }    double llt;
     int s1, s2;
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    double bbh, survp;
           for(theta=1; theta <=npar; theta++)    /*extern weight */
             trgradg[j][theta]=gradg[theta][j];    /* We are differentiating ll according to initial status */
            /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    /*for(i=1;i<imx;i++) 
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);      printf(" %d\n",s[4][i]);
            */
         pmij(pmmij,cov,ncovmodel,x,nlstate);    cov[1]=1.;
          
         k=0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(i=1; i<=(nlstate); i++){  
           for(j=1; j<=(nlstate+ndeath);j++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             k=k+1;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             mu[k][(int) age]=pmmij[i][j];      for(mi=1; mi<= wav[i]-1; mi++){
           }        for (ii=1;ii<=nlstate+ndeath;ii++)
         }          for (j=1;j<=nlstate+ndeath;j++){
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
             varpij[i][j][(int)age] = doldm[i][j];          }
         for(d=0; d<dh[mi][i]; d++){
         /*printf("\n%d ",(int)age);          newm=savm;
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          for (kk=1; kk<=cptcovage;kk++) {
      }*/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
         fprintf(ficresprob,"\n%d ",(int)age);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         fprintf(ficresprobcov,"\n%d ",(int)age);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         fprintf(ficresprobcor,"\n%d ",(int)age);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));          savm=oldm;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          oldm=newm;
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);        } /* end mult */
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);        
         }        s1=s[mw[mi][i]][i];
         i=0;        s2=s[mw[mi+1][i]][i];
         for (k=1; k<=(nlstate);k++){        bbh=(double)bh[mi][i]/(double)stepm; 
           for (l=1; l<=(nlstate+ndeath);l++){        /* bias is positive if real duration
             i=i++;         * is higher than the multiple of stepm and negative otherwise.
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);         */
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
             for (j=1; j<=i;j++){          lli=log(out[s1][s2] - savm[s1][s2]);
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);        } else if  (s2==-2) {
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));          for (j=1,survp=0. ; j<=nlstate; j++) 
             }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           }          lli= log(survp);
         }/* end of loop for state */        }else if (mle==1){
       } /* end of loop for age */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        } else if(mle==2){
       for (k1=1; k1<=(nlstate);k1++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         for (l1=1; l1<=(nlstate+ndeath);l1++){        } else if(mle==3){  /* exponential inter-extrapolation */
           if(l1==k1) continue;          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 */
           i=(k1-1)*(nlstate+ndeath)+l1;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           for (k2=1; k2<=(nlstate);k2++){          lli=log(out[s1][s2]); /* Original formula */
             for (l2=1; l2<=(nlstate+ndeath);l2++){        } else{  /* mle=0 back to 1 */
               if(l2==k2) continue;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
               j=(k2-1)*(nlstate+ndeath)+l2;          /*lli=log(out[s1][s2]); */ /* Original formula */
               if(j<=i) continue;        } /* End of if */
               for (age=bage; age<=fage; age ++){        ipmx +=1;
                 if ((int)age %5==0){        sw += weight[i];
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;        /*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]); */
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;        if(globpr){
                   mu1=mu[i][(int) age]/stepm*YEARM ;          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
                   mu2=mu[j][(int) age]/stepm*YEARM;   %11.6f %11.6f %11.6f ", \
                   /* Computing eigen value of matrix of covariance */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);            llt +=ll[k]*gipmx/gsw;
                   /* Eigen vectors */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));          }
                   v21=sqrt(1.-v11*v11);          fprintf(ficresilk," %10.6f\n", -llt);
                   v12=-v21;        }
                   v22=v11;      } /* end of wave */
                   /*printf(fignu*/    } /* end of individual */
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   if(first==1){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                     first=0;    if(globpr==0){ /* First time we count the contributions and weights */
                     fprintf(ficgp,"\nset parametric;set nolabel");      gipmx=ipmx;
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);      gsw=sw;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    }
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);    return -l;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);  }
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  /*************** function likelione ***********/
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  {
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    /* This routine should help understanding what is done with 
                   }else{       the selection of individuals/waves and
                     first=0;       to check the exact contribution to the likelihood.
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);       Plotting could be done.
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);     */
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    int k;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    if(*globpri !=0){ /* Just counts and sums, no printings */
                   }/* if first */      strcpy(fileresilk,"ilk"); 
                 } /* age mod 5 */      strcat(fileresilk,fileres);
               } /* end loop age */      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);        printf("Problem with resultfile: %s\n", fileresilk);
               first=1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
             } /*l12 */      }
           } /* k12 */      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");
         } /*l1 */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       }/* k1 */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     } /* loop covariates */      for(k=1; k<=nlstate; k++) 
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    }
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    *fretone=(*funcone)(p);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    if(*globpri !=0){
   }      fclose(ficresilk);
   free_vector(xp,1,npar);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   fclose(ficresprob);      fflush(fichtm); 
   fclose(ficresprobcov);    } 
   fclose(ficresprobcor);    return;
   fclose(ficgp);  }
   fclose(fichtm);  
 }  
   /*********** Maximum Likelihood Estimation ***************/
   
 /******************* Printing html file ***********/  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  {
                   int lastpass, int stepm, int weightopt, char model[],\    int i,j, iter=0;
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    double **xi;
                   int popforecast, int estepm ,\    double fret;
                   double jprev1, double mprev1,double anprev1, \    double fretone; /* Only one call to likelihood */
                   double jprev2, double mprev2,double anprev2){    /*  char filerespow[FILENAMELENGTH];*/
   int jj1, k1, i1, cpt;  
   /*char optionfilehtm[FILENAMELENGTH];*/  #ifdef NLOPT
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    int creturn;
     printf("Problem with %s \n",optionfilehtm), exit(0);    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 *\/ */
     double *lb;
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    double minf; /* the minimum objective value, upon return */
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    double * p1; /* Shifted parameters from 0 instead of 1 */
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    myfunc_data dinst, *d = &dinst;
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n  #endif
  - Life expectancies by age and initial health status (estepm=%2d months):  
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n      for (j=1;j<=npar;j++)
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n        xi[i][j]=(i==j ? 1.0 : 0.0);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    printf("Powell\n");  fprintf(ficlog,"Powell\n");
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    strcpy(filerespow,"pow"); 
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    strcat(filerespow,fileres);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    if((ficrespow=fopen(filerespow,"w"))==NULL) {
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n      printf("Problem with resultfile: %s\n", filerespow);
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
  if(popforecast==1) fprintf(fichtm,"\n    fprintf(ficrespow,"# Powell\n# iter -2*LL");
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    for (i=1;i<=nlstate;i++)
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      for(j=1;j<=nlstate+ndeath;j++)
         <br>",fileres,fileres,fileres,fileres);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
  else    fprintf(ficrespow,"\n");
    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);  #ifdef POWELL
 fprintf(fichtm," <li>Graphs</li><p>");    powell(p,xi,npar,ftol,&iter,&fret,func);
   #endif
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  #ifdef NLOPT
   #ifdef NEWUOA
  jj1=0;    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
  for(k1=1; k1<=m;k1++){  #else
    for(i1=1; i1<=ncodemax[k1];i1++){    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
      jj1++;  #endif
      if (cptcovn > 0) {    lb=vector(0,npar-1);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
        for (cpt=1; cpt<=cptcoveff;cpt++)    nlopt_set_lower_bounds(opt, lb);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    nlopt_set_initial_step1(opt, 0.1);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    
      }    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
      /* Pij */    d->function = func;
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        nlopt_set_min_objective(opt, myfunc, d);
      /* Quasi-incidences */    nlopt_set_xtol_rel(opt, ftol);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      printf("nlopt failed! %d\n",creturn); 
        /* Stable prevalence in each health state */    }
        for(cpt=1; cpt<nlstate;cpt++){    else {
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
        }      iter=1; /* not equal */
     for(cpt=1; cpt<=nlstate;cpt++) {    }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    nlopt_destroy(opt);
 interval) in state (%d): v%s%d%d.png <br>  #endif
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      free_matrix(xi,1,npar,1,npar);
      }    fclose(ficrespow);
      for(cpt=1; cpt<=nlstate;cpt++) {    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  }
 health expectancies in states (1) and (2): e%s%d.png<br>  
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  /**** Computes Hessian and covariance matrix ***/
    }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
  }  {
 fclose(fichtm);    double  **a,**y,*x,pd;
 }    double **hess;
     int i, j;
 /******************* Gnuplot file **************/    int *indx;
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   int ng;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    void ludcmp(double **a, int npar, int *indx, double *d) ;
     printf("Problem with file %s",optionfilegnuplot);    double gompertz(double p[]);
   }    hess=matrix(1,npar,1,npar);
   
 #ifdef windows    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficgp,"cd \"%s\" \n",pathc);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 #endif    for (i=1;i<=npar;i++){
 m=pow(2,cptcoveff);      printf("%d",i);fflush(stdout);
        fprintf(ficlog,"%d",i);fflush(ficlog);
  /* 1eme*/     
   for (cpt=1; cpt<= nlstate ; cpt ++) {       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
    for (k1=1; k1<= m ; k1 ++) {      
       /*  printf(" %f ",p[i]);
 #ifdef windows          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    }
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    
 #endif    for (i=1;i<=npar;i++) {
 #ifdef unix      for (j=1;j<=npar;j++)  {
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        if (j>i) { 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          printf(".%d%d",i,j);fflush(stdout);
 #endif          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
 for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          hess[j][i]=hess[i][j];    
   else fprintf(ficgp," \%%*lf (\%%*lf)");          /*printf(" %lf ",hess[i][j]);*/
 }        }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      }
     for (i=1; i<= nlstate ; i ++) {    }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    printf("\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficlog,"\n");
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      for (i=1; i<= nlstate ; i ++) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    a=matrix(1,npar,1,npar);
 }      y=matrix(1,npar,1,npar);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    x=vector(1,npar);
 #ifdef unix    indx=ivector(1,npar);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    for (i=1;i<=npar;i++)
 #endif      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
    }    ludcmp(a,npar,indx,&pd);
   }  
   /*2 eme*/    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   for (k1=1; k1<= m ; k1 ++) {      x[j]=1;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      lubksb(a,npar,indx,x);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      for (i=1;i<=npar;i++){ 
            matcov[i][j]=x[i];
     for (i=1; i<= nlstate+1 ; i ++) {      }
       k=2*i;    }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    printf("\n#Hessian matrix#\n");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficlog,"\n#Hessian matrix#\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (i=1;i<=npar;i++) { 
 }        for (j=1;j<=npar;j++) { 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        printf("%.3e ",hess[i][j]);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        fprintf(ficlog,"%.3e ",hess[i][j]);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      }
       for (j=1; j<= nlstate+1 ; j ++) {      printf("\n");
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficlog,"\n");
         else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");    /* Recompute Inverse */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    for (i=1;i<=npar;i++)
       for (j=1; j<= nlstate+1 ; j ++) {      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    ludcmp(a,npar,indx,&pd);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      /*  printf("\n#Hessian matrix recomputed#\n");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");    for (j=1;j<=npar;j++) {
     }      for (i=1;i<=npar;i++) x[i]=0;
   }      x[j]=1;
        lubksb(a,npar,indx,x);
   /*3eme*/      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
   for (k1=1; k1<= m ; k1 ++) {        printf("%.3e ",y[i][j]);
     for (cpt=1; cpt<= nlstate ; cpt ++) {        fprintf(ficlog,"%.3e ",y[i][j]);
       k=2+nlstate*(2*cpt-2);      }
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      printf("\n");
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      fprintf(ficlog,"\n");
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    free_matrix(a,1,npar,1,npar);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    free_matrix(y,1,npar,1,npar);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
 */    free_matrix(hess,1,npar,1,npar);
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);  
   }
       }  
     }  /*************** hessian matrix ****************/
   }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
    {
   /* CV preval stat */    int i;
     for (k1=1; k1<= m ; k1 ++) {    int l=1, lmax=20;
     for (cpt=1; cpt<nlstate ; cpt ++) {    double k1,k2;
       k=3;    double p2[MAXPARM+1]; /* identical to x */
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    double res;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
       for (i=1; i< nlstate ; i ++)    int k=0,kmax=10;
         fprintf(ficgp,"+$%d",k+i+1);    double l1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
          fx=func(x);
       l=3+(nlstate+ndeath)*cpt;    for (i=1;i<=npar;i++) p2[i]=x[i];
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       for (i=1; i< nlstate ; i ++) {      l1=pow(10,l);
         l=3+(nlstate+ndeath)*cpt;      delts=delt;
         fprintf(ficgp,"+$%d",l+i+1);      for(k=1 ; k <kmax; k=k+1){
       }        delt = delta*(l1*k);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          p2[theta]=x[theta] +delt;
     }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   }          p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
   /* proba elementaires */        /*res= (k1-2.0*fx+k2)/delt/delt; */
    for(i=1,jk=1; i <=nlstate; i++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     for(k=1; k <=(nlstate+ndeath); k++){        
       if (k != i) {  #ifdef DEBUGHESS
         for(j=1; j <=ncovmodel; j++){        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
                fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  #endif
           jk++;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           fprintf(ficgp,"\n");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         }          k=kmax;
       }        }
     }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
    }          k=kmax; l=lmax*10;
         }
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
      for(jk=1; jk <=m; jk++) {          delts=delt;
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);        }
        if (ng==2)      }
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    }
        else    delti[theta]=delts;
          fprintf(ficgp,"\nset title \"Probability\"\n");    return res; 
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    
        i=1;  }
        for(k2=1; k2<=nlstate; k2++) {  
          k3=i;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
          for(k=1; k<=(nlstate+ndeath); k++) {  {
            if (k != k2){    int i;
              if(ng==2)    int l=1, lmax=20;
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    double k1,k2,k3,k4,res,fx;
              else    double p2[MAXPARM+1];
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    int k;
              ij=1;  
              for(j=3; j <=ncovmodel; j++) {    fx=func(x);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    for (k=1; k<=2; k++) {
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      for (i=1;i<=npar;i++) p2[i]=x[i];
                  ij++;      p2[thetai]=x[thetai]+delti[thetai]/k;
                }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                else      k1=func(p2)-fx;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    
              }      p2[thetai]=x[thetai]+delti[thetai]/k;
              fprintf(ficgp,")/(1");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                    k2=func(p2)-fx;
              for(k1=1; k1 <=nlstate; k1++){      
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      p2[thetai]=x[thetai]-delti[thetai]/k;
                ij=1;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                for(j=3; j <=ncovmodel; j++){      k3=func(p2)-fx;
                  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]]]);      p2[thetai]=x[thetai]-delti[thetai]/k;
                    ij++;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                  }      k4=func(p2)-fx;
                  else      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  #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(ficgp,")");      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
              }  #endif
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    }
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    return res;
              i=i+ncovmodel;  }
            }  
          }  /************** Inverse of matrix **************/
        }  void ludcmp(double **a, int n, int *indx, double *d) 
      }  { 
    }    int i,imax,j,k; 
    fclose(ficgp);    double big,dum,sum,temp; 
 }  /* end gnuplot */    double *vv; 
    
     vv=vector(1,n); 
 /*************** Moving average **************/    *d=1.0; 
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    for (i=1;i<=n;i++) { 
       big=0.0; 
   int i, cpt, cptcod;      for (j=1;j<=n;j++) 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
       for (i=1; i<=nlstate;i++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      vv[i]=1.0/big; 
           mobaverage[(int)agedeb][i][cptcod]=0.;    } 
        for (j=1;j<=n;j++) { 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      for (i=1;i<j;i++) { 
       for (i=1; i<=nlstate;i++){        sum=a[i][j]; 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           for (cpt=0;cpt<=4;cpt++){        a[i][j]=sum; 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      } 
           }      big=0.0; 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      for (i=j;i<=n;i++) { 
         }        sum=a[i][j]; 
       }        for (k=1;k<j;k++) 
     }          sum -= a[i][k]*a[k][j]; 
            a[i][j]=sum; 
 }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
           imax=i; 
 /************** Forecasting ******************/        } 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){      } 
        if (j != imax) { 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for (k=1;k<=n;k++) { 
   int *popage;          dum=a[imax][k]; 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          a[imax][k]=a[j][k]; 
   double *popeffectif,*popcount;          a[j][k]=dum; 
   double ***p3mat;        } 
   char fileresf[FILENAMELENGTH];        *d = -(*d); 
         vv[imax]=vv[j]; 
  agelim=AGESUP;      } 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      if (j != n) { 
          dum=1.0/(a[j][j]); 
          for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   strcpy(fileresf,"f");      } 
   strcat(fileresf,fileres);    } 
   if((ficresf=fopen(fileresf,"w"))==NULL) {    free_vector(vv,1,n);  /* Doesn't work */
     printf("Problem with forecast resultfile: %s\n", fileresf);  ;
   }  } 
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   void lubksb(double **a, int n, int *indx, double b[]) 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  { 
     int i,ii=0,ip,j; 
   if (mobilav==1) {    double sum; 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
     movingaverage(agedeb, fage, ageminpar, mobaverage);    for (i=1;i<=n;i++) { 
   }      ip=indx[i]; 
       sum=b[ip]; 
   stepsize=(int) (stepm+YEARM-1)/YEARM;      b[ip]=b[i]; 
   if (stepm<=12) stepsize=1;      if (ii) 
          for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   agelim=AGESUP;      else if (sum) ii=i; 
        b[i]=sum; 
   hstepm=1;    } 
   hstepm=hstepm/stepm;    for (i=n;i>=1;i--) { 
   yp1=modf(dateintmean,&yp);      sum=b[i]; 
   anprojmean=yp;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   yp2=modf((yp1*12),&yp);      b[i]=sum/a[i][i]; 
   mprojmean=yp;    } 
   yp1=modf((yp2*30.5),&yp);  } 
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;  void pstamp(FILE *fichier)
   if(mprojmean==0) jprojmean=1;  {
      fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  }
    
   for(cptcov=1;cptcov<=i2;cptcov++){  /************ Frequencies ********************/
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  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[])
       k=k+1;  {  /* Some frequencies */
       fprintf(ficresf,"\n#******");    
       for(j=1;j<=cptcoveff;j++) {    int i, m, jk, j1, bool, z1,j;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int first;
       }    double ***freq; /* Frequencies */
       fprintf(ficresf,"******\n");    double *pp, **prop;
       fprintf(ficresf,"# StartingAge FinalAge");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    char fileresp[FILENAMELENGTH];
          
          pp=vector(1,nlstate);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
         fprintf(ficresf,"\n");    strcpy(fileresp,"p");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      printf("Problem with prevalence resultfile: %s\n", fileresp);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           nhstepm = nhstepm/hstepm;      exit(0);
              }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
           oldm=oldms;savm=savms;    j1=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
            j=cptcoveff;
           for (h=0; h<=nhstepm; h++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    first=1;
             }  
             for(j=1; j<=nlstate+ndeath;j++) {    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
               kk1=0.;kk2=0;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
               for(i=1; i<=nlstate;i++) {                  /*    j1++; */
                 if (mobilav==1)    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                 else {          scanf("%d", i);*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        for (i=-5; i<=nlstate+ndeath; i++)  
                 }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
                            for(m=iagemin; m <= iagemax+3; m++)
               }              freq[i][jk][m]=0;
               if (h==(int)(calagedate+12*cpt)){        
                 fprintf(ficresf," %.3f", kk1);        for (i=1; i<=nlstate; i++)  
                                  for(m=iagemin; m <= iagemax+3; m++)
               }            prop[i][m]=0;
             }        
           }        dateintsum=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        k2cpt=0;
         }        for (i=1; i<=imx; i++) {
       }          bool=1;
     }          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
   }            for (z1=1; z1<=cptcoveff; z1++)       
                      if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                 bool=0;
   fclose(ficresf);                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
 }                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
 /************** Forecasting ******************/                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
 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){                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                } 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          }
   int *popage;   
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          if (bool==1){
   double *popeffectif,*popcount;            for(m=firstpass; m<=lastpass; m++){
   double ***p3mat,***tabpop,***tabpopprev;              k2=anint[m][i]+(mint[m][i]/12.);
   char filerespop[FILENAMELENGTH];              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   agelim=AGESUP;                if (m<lastpass) {
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                    freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                }
                  
                  if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   strcpy(filerespop,"pop");                  dateintsum=dateintsum+k2;
   strcat(filerespop,fileres);                  k2cpt++;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {                }
     printf("Problem with forecast resultfile: %s\n", filerespop);                /*}*/
   }            }
   printf("Computing forecasting: result on file '%s' \n", filerespop);          }
         } /* end i */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   if (mobilav==1) {        pstamp(ficresp);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        if  (cptcovn>0) {
     movingaverage(agedeb, fage, ageminpar, mobaverage);          fprintf(ficresp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficlog, "\n#********** Variable "); 
   if (stepm<=12) stepsize=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficlog, "**********\n#");
   agelim=AGESUP;        }
          for(i=1; i<=nlstate;i++) 
   hstepm=1;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   hstepm=hstepm/stepm;        fprintf(ficresp, "\n");
          
   if (popforecast==1) {        for(i=iagemin; i <= iagemax+3; i++){
     if((ficpop=fopen(popfile,"r"))==NULL) {          if(i==iagemax+3){
       printf("Problem with population file : %s\n",popfile);exit(0);            fprintf(ficlog,"Total");
     }          }else{
     popage=ivector(0,AGESUP);            if(first==1){
     popeffectif=vector(0,AGESUP);              first=0;
     popcount=vector(0,AGESUP);              printf("See log file for details...\n");
                }
     i=1;              fprintf(ficlog,"Age %d", i);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          }
              for(jk=1; jk <=nlstate ; jk++){
     imx=i;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];              pp[jk] += freq[jk][m][i]; 
   }          }
           for(jk=1; jk <=nlstate ; jk++){
   for(cptcov=1;cptcov<=i2;cptcov++){            for(m=-1, pos=0; m <=0 ; m++)
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              pos += freq[jk][m][i];
       k=k+1;            if(pp[jk]>=1.e-10){
       fprintf(ficrespop,"\n#******");              if(first==1){
       for(j=1;j<=cptcoveff;j++) {                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }
       }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fprintf(ficrespop,"******\n");            }else{
       fprintf(ficrespop,"# Age");              if(first==1)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       if (popforecast==1)  fprintf(ficrespop," [Population]");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                  }
       for (cpt=0; cpt<=0;cpt++) {          }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
                  for(jk=1; jk <=nlstate ; jk++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              pp[jk] += freq[jk][m][i];
           nhstepm = nhstepm/hstepm;          }       
                    for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            pos += pp[jk];
           oldm=oldms;savm=savms;            posprop += prop[jk][i];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
                  for(jk=1; jk <=nlstate ; jk++){
           for (h=0; h<=nhstepm; h++){            if(pos>=1.e-5){
             if (h==(int) (calagedate+YEARM*cpt)) {              if(first==1)
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                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);
             for(j=1; j<=nlstate+ndeath;j++) {            }else{
               kk1=0.;kk2=0;              if(first==1)
               for(i=1; i<=nlstate;i++) {                              printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                 if (mobilav==1)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            }
                 else {            if( i <= iagemax){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              if(pos>=1.e-5){
                 }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
               }                /*probs[i][jk][j1]= pp[jk]/pos;*/
               if (h==(int)(calagedate+12*cpt)){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;              }
                   /*fprintf(ficrespop," %.3f", kk1);              else
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
               }            }
             }          }
             for(i=1; i<=nlstate;i++){          
               kk1=0.;          for(jk=-1; jk <=nlstate+ndeath; jk++)
                 for(j=1; j<=nlstate;j++){            for(m=-1; m <=nlstate+ndeath; m++)
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];              if(freq[jk][m][i] !=0 ) {
                 }              if(first==1)
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
             }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          if(i <= iagemax)
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            fprintf(ficresp,"\n");
           }          if(first==1)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            printf("Others in log...\n");
         }          fprintf(ficlog,"\n");
       }        }
          /*}*/
   /******/    }
     dateintmean=dateintsum/k2cpt; 
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {   
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fclose(ficresp);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_vector(pp,1,nlstate);
           nhstepm = nhstepm/hstepm;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
              /* End of Freq */
           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);    /************ Prevalence ********************/
           for (h=0; h<=nhstepm; h++){  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 (h==(int) (calagedate+YEARM*cpt)) {  {  
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    /* 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).
             for(j=1; j<=nlstate+ndeath;j++) {       We still use firstpass and lastpass as another selection.
               kk1=0.;kk2=0;    */
               for(i=1; i<=nlstate;i++) {                 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        int i, m, jk, j1, bool, z1,j;
               }  
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    double **prop;
             }    double posprop; 
           }    double  y2; /* in fractional years */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int iagemin, iagemax;
         }    int first; /** to stop verbosity which is redirected to log file */
       }  
    }    iagemin= (int) agemin;
   }    iagemax= (int) agemax;
      /*pp=vector(1,nlstate);*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if (popforecast==1) {    j1=0;
     free_ivector(popage,0,AGESUP);    
     free_vector(popeffectif,0,AGESUP);    /*j=cptcoveff;*/
     free_vector(popcount,0,AGESUP);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }    
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    first=1;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   fclose(ficrespop);      /*for(i1=1; i1<=ncodemax[k1];i1++){
 }        j1++;*/
         
 /***********************************************/        for (i=1; i<=nlstate; i++)  
 /**************** Main Program *****************/          for(m=iagemin; m <= iagemax+3; m++)
 /***********************************************/            prop[i][m]=0.0;
        
 int main(int argc, char *argv[])        for (i=1; i<=imx; i++) { /* Each individual */
 {          bool=1;
           if  (cptcovn>0) {
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            for (z1=1; z1<=cptcoveff; z1++) 
   double agedeb, agefin,hf;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                bool=0;
           } 
   double fret;          if (bool==1) { 
   double **xi,tmp,delta;            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 */
   double dum; /* Dummy variable */              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   double ***p3mat;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   int *indx;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   char line[MAXLINE], linepar[MAXLINE];                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); 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   int firstobs=1, lastobs=10;                  /*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]]);*/
   int sdeb, sfin; /* Status at beginning and end */                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   int c,  h , cpt,l;                  prop[s[m][i]][iagemax+3] += weight[i]; 
   int ju,jl, mi;                } 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            } /* end selection of waves */
   int mobilav=0,popforecast=0;          }
   int hstepm, nhstepm;        }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   double bage, fage, age, agelim, agebase;            posprop += prop[jk][i]; 
   double ftolpl=FTOL;          } 
   double **prlim;          
   double *severity;          for(jk=1; jk <=nlstate ; jk++){     
   double ***param; /* Matrix of parameters */            if( i <=  iagemax){ 
   double  *p;              if(posprop>=1.e-5){ 
   double **matcov; /* Matrix of covariance */                probs[i][jk][j1]= prop[jk][i]/posprop;
   double ***delti3; /* Scale */              } else{
   double *delti; /* Scale */                if(first==1){
   double ***eij, ***vareij;                  first=0;
   double **varpl; /* Variances of prevalence limits by age */                  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]);
   double *epj, vepp;                }
   double kk1, kk2;              }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;            } 
            }/* end jk */ 
         }/* end i */ 
   char *alph[]={"a","a","b","c","d","e"}, str[4];      /*} *//* end i1 */
     } /* end j1 */
     
   char z[1]="c", occ;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 #include <sys/time.h>    /*free_vector(pp,1,nlstate);*/
 #include <time.h>    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  }  /* End of prevalence */
    
   /* long total_usecs;  /************* Waves Concatenation ***************/
   struct timeval start_time, end_time;  
    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)
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  {
   getcwd(pathcd, size);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
   printf("\n%s",version);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   if(argc <=1){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     printf("\nEnter the parameter file name: ");       and mw[mi+1][i]. dh depends on stepm.
     scanf("%s",pathtot);       */
   }  
   else{    int i, mi, m;
     strcpy(pathtot,argv[1]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   }       double sum=0., jmean=0.;*/
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    int first;
   /*cygwin_split_path(pathtot,path,optionfile);    int j, k=0,jk, ju, jl;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    double sum=0.;
   /* cutv(path,optionfile,pathtot,'\\');*/    first=0;
     jmin=100000;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    jmax=-1;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    jmean=0.;
   chdir(path);    for(i=1; i<=imx; i++){
   replace(pathc,path);      mi=0;
       m=firstpass;
 /*-------- arguments in the command line --------*/      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   strcpy(fileres,"r");          mw[++mi][i]=m;
   strcat(fileres, optionfilefiname);        if(m >=lastpass)
   strcat(fileres,".txt");    /* Other files have txt extension */          break;
         else
   /*---------arguments file --------*/          m++;
       }/* end while */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      if (s[m][i] > nlstate){
     printf("Problem with optionfile %s\n",optionfile);        mi++;     /* Death is another wave */
     goto end;        /* if(mi==0)  never been interviewed correctly before death */
   }           /* Only death is a correct wave */
         mw[mi][i]=m;
   strcpy(filereso,"o");      }
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {      wav[i]=mi;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      if(mi==0){
   }        nbwarn++;
         if(first==0){
   /* Reads comments: lines beginning with '#' */          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   while((c=getc(ficpar))=='#' && c!= EOF){          first=1;
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        if(first==1){
     puts(line);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     fputs(line,ficparo);        }
   }      } /* end mi==0 */
   ungetc(c,ficpar);    } /* End individuals */
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    for(i=1; i<=imx; i++){
   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);      for(mi=1; mi<wav[i];mi++){
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);        if (stepm <=0)
 while((c=getc(ficpar))=='#' && c!= EOF){          dh[mi][i]=1;
     ungetc(c,ficpar);        else{
     fgets(line, MAXLINE, ficpar);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     puts(line);            if (agedc[i] < 2*AGESUP) {
     fputs(line,ficparo);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   }              if(j==0) j=1;  /* Survives at least one month after exam */
   ungetc(c,ficpar);              else if(j<0){
                  nberr++;
                    printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   covar=matrix(0,NCOVMAX,1,n);                j=1; /* Temporary Dangerous patch */
   cptcovn=0;                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);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                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);
   ncovmodel=2+cptcovn;              }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */              k=k+1;
                if (j >= jmax){
   /* Read guess parameters */                jmax=j;
   /* Reads comments: lines beginning with '#' */                ijmax=i;
   while((c=getc(ficpar))=='#' && c!= EOF){              }
     ungetc(c,ficpar);              if (j <= jmin){
     fgets(line, MAXLINE, ficpar);                jmin=j;
     puts(line);                ijmin=i;
     fputs(line,ficparo);              }
   }              sum=sum+j;
   ungetc(c,ficpar);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            }
     for(i=1; i <=nlstate; i++)          }
     for(j=1; j <=nlstate+ndeath-1; j++){          else{
       fscanf(ficpar,"%1d%1d",&i1,&j1);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficparo,"%1d%1d",i1,j1);  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){            k=k+1;
         fscanf(ficpar," %lf",&param[i][j][k]);            if (j >= jmax) {
         printf(" %lf",param[i][j][k]);              jmax=j;
         fprintf(ficparo," %lf",param[i][j][k]);              ijmax=i;
       }            }
       fscanf(ficpar,"\n");            else if (j <= jmin){
       printf("\n");              jmin=j;
       fprintf(ficparo,"\n");              ijmin=i;
     }            }
              /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
   p=param[1][1];              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]);
   /* Reads comments: lines beginning with '#' */              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]);
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);            sum=sum+j;
     fgets(line, MAXLINE, ficpar);          }
     puts(line);          jk= j/stepm;
     fputs(line,ficparo);          jl= j -jk*stepm;
   }          ju= j -(jk+1)*stepm;
   ungetc(c,ficpar);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              dh[mi][i]=jk;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */              bh[mi][i]=0;
   for(i=1; i <=nlstate; i++){            }else{ /* We want a negative bias in order to only have interpolation ie
     for(j=1; j <=nlstate+ndeath-1; j++){                    * to avoid the price of an extra matrix product in likelihood */
       fscanf(ficpar,"%1d%1d",&i1,&j1);              dh[mi][i]=jk+1;
       printf("%1d%1d",i,j);              bh[mi][i]=ju;
       fprintf(ficparo,"%1d%1d",i1,j1);            }
       for(k=1; k<=ncovmodel;k++){          }else{
         fscanf(ficpar,"%le",&delti3[i][j][k]);            if(jl <= -ju){
         printf(" %le",delti3[i][j][k]);              dh[mi][i]=jk;
         fprintf(ficparo," %le",delti3[i][j][k]);              bh[mi][i]=jl;       /* bias is positive if real duration
       }                                   * is higher than the multiple of stepm and negative otherwise.
       fscanf(ficpar,"\n");                                   */
       printf("\n");            }
       fprintf(ficparo,"\n");            else{
     }              dh[mi][i]=jk+1;
   }              bh[mi][i]=ju;
   delti=delti3[1][1];            }
              if(dh[mi][i]==0){
   /* Reads comments: lines beginning with '#' */              dh[mi][i]=1; /* At least one step */
   while((c=getc(ficpar))=='#' && c!= EOF){              bh[mi][i]=ju; /* At least one step */
     ungetc(c,ficpar);              /*  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);*/
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          } /* end if mle */
     fputs(line,ficparo);        }
   }      } /* end wave */
   ungetc(c,ficpar);    }
      jmean=sum/k;
   matcov=matrix(1,npar,1,npar);    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);
   for(i=1; i <=npar; i++){    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);
     fscanf(ficpar,"%s",&str);   }
     printf("%s",str);  
     fprintf(ficparo,"%s",str);  /*********** Tricode ****************************/
     for(j=1; j <=i; j++){  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
       fscanf(ficpar," %le",&matcov[i][j]);  {
       printf(" %.5le",matcov[i][j]);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       fprintf(ficparo," %.5le",matcov[i][j]);    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     }     * Boring subroutine which should only output nbcode[Tvar[j]][k]
     fscanf(ficpar,"\n");     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     printf("\n");     * nbcode[Tvar[j]][1]= 
     fprintf(ficparo,"\n");    */
   }  
   for(i=1; i <=npar; i++)    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     for(j=i+1;j<=npar;j++)    int modmaxcovj=0; /* Modality max of covariates j */
       matcov[i][j]=matcov[j][i];    int cptcode=0; /* Modality max of covariates j */
        int modmincovj=0; /* Modality min of covariates j */
   printf("\n");  
   
     cptcoveff=0; 
     /*-------- Rewriting paramater file ----------*/   
      strcpy(rfileres,"r");    /* "Rparameterfile */    for (k=-1; k < maxncov; k++) Ndum[k]=0;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    /* Loop on covariates without age and products */
     if((ficres =fopen(rfileres,"w"))==NULL) {    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      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(ficres,"#%s\n",version);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                          * If product of Vn*Vm, still boolean *:
     /*-------- data file ----------*/                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
     if((fic=fopen(datafile,"r"))==NULL)    {                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
       printf("Problem with datafile: %s\n", datafile);goto end;        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     }                                        modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
     n= lastobs;          modmaxcovj=ij; 
     severity = vector(1,maxwav);        else if (ij < modmincovj) 
     outcome=imatrix(1,maxwav+1,1,n);          modmincovj=ij; 
     num=ivector(1,n);        if ((ij < -1) && (ij > NCOVMAX)){
     moisnais=vector(1,n);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
     annais=vector(1,n);          exit(1);
     moisdc=vector(1,n);        }else
     andc=vector(1,n);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     agedc=vector(1,n);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     cod=ivector(1,n);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     weight=vector(1,n);        /* getting the maximum value of the modality of the covariate
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
     mint=matrix(1,maxwav,1,n);           female is 1, then modmaxcovj=1.*/
     anint=matrix(1,maxwav,1,n);      }
     s=imatrix(1,maxwav+1,1,n);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     adl=imatrix(1,maxwav+1,1,n);          cptcode=modmaxcovj;
     tab=ivector(1,NCOVMAX);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     ncodemax=ivector(1,8);     /*for (i=0; i<=cptcode; i++) {*/
       for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
     i=1;        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
     while (fgets(line, MAXLINE, fic) != NULL)    {        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
       if ((i >= firstobs) && (i <=lastobs)) {          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
                }
         for (j=maxwav;j>=1;j--){        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           strcpy(line,stra);      } /* Ndum[-1] number of undefined modalities */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
         }      /* 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;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);         modmincovj=3; modmaxcovj = 7;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
          which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);         variables V1_1 and V1_2.
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);         nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);         nbcode[Tvar[j]][2]=1;
         for (j=ncovcol;j>=1;j--){         nbcode[Tvar[j]][3]=2;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      */
         }      ij=1; /* ij is similar to i but can jumps over null modalities */
         num[i]=atol(stra);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
                for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          /*recode from 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])); ij=ij+1;}*/          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. 
         i=i+1;                                       k is a modality. If we have model=V1+V1*sex 
       }                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     }            ij++;
     /* printf("ii=%d", ij);          }
        scanf("%d",i);*/          if (ij > ncodemax[j]) break; 
   imx=i-1; /* Number of individuals */        }  /* end of loop on */
       } /* end of loop on modality */ 
   /* for (i=1; i<=imx; i++){    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    
     }*/    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
    /*  for (i=1; i<=imx; i++){     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
      if (s[4][i]==9)  s[4][i]=-1;     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      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]));}*/     Ndum[ij]++; 
     } 
    
   /* Calculation of the number of parameter from char model*/   ij=1;
   Tvar=ivector(1,15);   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   Tprod=ivector(1,15);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   Tvaraff=ivector(1,15);     if((Ndum[i]!=0) && (i<=ncovcol)){
   Tvard=imatrix(1,15,1,2);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   Tage=ivector(1,15);             Tvaraff[ij]=i; /*For printing (unclear) */
           ij++;
   if (strlen(model) >1){     }else
     j=0, j1=0, k1=1, k2=1;         Tvaraff[ij]=0;
     j=nbocc(model,'+');   }
     j1=nbocc(model,'*');   ij--;
     cptcovn=j+1;   cptcoveff=ij; /*Number of total covariates*/
     cptcovprod=j1;  
      }
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);  /*********** Health Expectancies ****************/
       goto end;  
     }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
      
     for(i=(j+1); i>=1;i--){  {
       cutv(stra,strb,modelsav,'+');    /* Health expectancies, no variances */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    int i, j, nhstepm, hstepm, h, nstepm;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    int nhstepma, nstepma; /* Decreasing with age */
       /*scanf("%d",i);*/    double age, agelim, hf;
       if (strchr(strb,'*')) {    double ***p3mat;
         cutv(strd,strc,strb,'*');    double eip;
         if (strcmp(strc,"age")==0) {  
           cptcovprod--;    pstamp(ficreseij);
           cutv(strb,stre,strd,'V');    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
           Tvar[i]=atoi(stre);    fprintf(ficreseij,"# Age");
           cptcovage++;    for(i=1; i<=nlstate;i++){
             Tage[cptcovage]=i;      for(j=1; j<=nlstate;j++){
             /*printf("stre=%s ", stre);*/        fprintf(ficreseij," e%1d%1d ",i,j);
         }      }
         else if (strcmp(strd,"age")==0) {      fprintf(ficreseij," e%1d. ",i);
           cptcovprod--;    }
           cutv(strb,stre,strc,'V');    fprintf(ficreseij,"\n");
           Tvar[i]=atoi(stre);  
           cptcovage++;    
           Tage[cptcovage]=i;    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
         else {    }
           cutv(strb,stre,strc,'V');    else  hstepm=estepm;   
           Tvar[i]=ncovcol+k1;    /* We compute the life expectancy from trapezoids spaced every estepm months
           cutv(strb,strc,strd,'V');     * This is mainly to measure the difference between two models: for example
           Tprod[k1]=i;     * if stepm=24 months pijx are given only every 2 years and by summing them
           Tvard[k1][1]=atoi(strc);     * we are calculating an estimate of the Life Expectancy assuming a linear 
           Tvard[k1][2]=atoi(stre);     * progression in between and thus overestimating or underestimating according
           Tvar[cptcovn+k2]=Tvard[k1][1];     * to the curvature of the survival function. If, for the same date, we 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           for (k=1; k<=lastobs;k++)     * to compare the new estimate of Life expectancy with the same linear 
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];     * hypothesis. A more precise result, taking into account a more precise
           k1++;     * curvature will be obtained if estepm is as small as stepm. */
           k2=k2+2;  
         }    /* 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. 
       else {       nhstepm is the number of hstepm from age to agelim 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/       nstepm is the number of stepm from age to agelin. 
        /*  scanf("%d",i);*/       Look at hpijx to understand the reason of that which relies in memory size
       cutv(strd,strc,strb,'V');       and note for a fixed period like estepm months */
       Tvar[i]=atoi(strc);    /* 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
       strcpy(modelsav,stra);         means that if the survival funtion is printed only each two years of age and if
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         scanf("%d",i);*/       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 */ 
    
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    agelim=AGESUP;
   printf("cptcovprod=%d ", cptcovprod);    /* If stepm=6 months */
   scanf("%d ",i);*/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     fclose(fic);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
     /*  if(mle==1){*/  /* nhstepm age range expressed in number of stepm */
     if (weightopt != 1) { /* Maximisation without weights*/    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       for(i=1;i<=n;i++) weight[i]=1.0;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     }    /* if (stepm >= YEARM) hstepm=1;*/
     /*-calculation of age at interview from date of interview and age at death -*/    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     agev=matrix(1,maxwav,1,imx);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (i=1; i<=imx; i++) {    for (age=bage; age<=fage; age ++){ 
       for(m=2; (m<= maxwav); m++) {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
          anint[m][i]=9999;      /* if (stepm >= YEARM) hstepm=1;*/
          s[m][i]=-1;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;      /* 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 */
       
     for (i=1; i<=imx; i++)  {      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      
       for(m=1; (m<= maxwav); m++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         if(s[m][i] >0){      
           if (s[m][i] >= nlstate+1) {      printf("%d|",(int)age);fflush(stdout);
             if(agedc[i]>0)      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
               if(moisdc[i]!=99 && andc[i]!=9999)      
                 agev[m][i]=agedc[i];      /* Computing expectancies */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      for(i=1; i<=nlstate;i++)
            else {        for(j=1; j<=nlstate;j++)
               if (andc[i]!=9999){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               agev[m][i]=-1;            
               }            /* 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]);*/
             }  
           }          }
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      fprintf(ficreseij,"%3.0f",age );
             if(mint[m][i]==99 || anint[m][i]==9999)      for(i=1; i<=nlstate;i++){
               agev[m][i]=1;        eip=0;
             else if(agev[m][i] <agemin){        for(j=1; j<=nlstate;j++){
               agemin=agev[m][i];          eip +=eij[i][j][(int)age];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
             }        }
             else if(agev[m][i] >agemax){        fprintf(ficreseij,"%9.4f", eip );
               agemax=agev[m][i];      }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      fprintf(ficreseij,"\n");
             }      
             /*agev[m][i]=anint[m][i]-annais[i];*/    }
             /*   agev[m][i] = age[i]+2*m;*/    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }    printf("\n");
           else { /* =9 */    fprintf(ficlog,"\n");
             agev[m][i]=1;    
             s[m][i]=-1;  }
           }  
         }  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
         else /*= 0 Unknown */  
           agev[m][i]=1;  {
       }    /* Covariances of health expectancies eij and of total life expectancies according
         to initial status i, ei. .
     }    */
     for (i=1; i<=imx; i++)  {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       for(m=1; (m<= maxwav); m++){    int nhstepma, nstepma; /* Decreasing with age */
         if (s[m][i] > (nlstate+ndeath)) {    double age, agelim, hf;
           printf("Error: Wrong value in nlstate or ndeath\n");      double ***p3matp, ***p3matm, ***varhe;
           goto end;    double **dnewm,**doldm;
         }    double *xp, *xm;
       }    double **gp, **gm;
     }    double ***gradg, ***trgradg;
     int theta;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
     double eip, vip;
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     free_vector(moisnais,1,n);    xp=vector(1,npar);
     free_vector(annais,1,n);    xm=vector(1,npar);
     /* free_matrix(mint,1,maxwav,1,n);    dnewm=matrix(1,nlstate*nlstate,1,npar);
        free_matrix(anint,1,maxwav,1,n);*/    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     free_vector(moisdc,1,n);    
     free_vector(andc,1,n);    pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
        fprintf(ficresstdeij,"# Age");
     wav=ivector(1,imx);    for(i=1; i<=nlstate;i++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      for(j=1; j<=nlstate;j++)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
          fprintf(ficresstdeij," e%1d. ",i);
     /* Concatenates waves */    }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
       Tcode=ivector(1,100);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    fprintf(ficrescveij,"# Age");
       ncodemax[1]=1;    for(i=1; i<=nlstate;i++)
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      for(j=1; j<=nlstate;j++){
              cptj= (j-1)*nlstate+i;
    codtab=imatrix(1,100,1,10);        for(i2=1; i2<=nlstate;i2++)
    h=0;          for(j2=1; j2<=nlstate;j2++){
    m=pow(2,cptcoveff);            cptj2= (j2-1)*nlstate+i2;
              if(cptj2 <= cptj)
    for(k=1;k<=cptcoveff; k++){              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
      for(i=1; i <=(m/pow(2,k));i++){          }
        for(j=1; j <= ncodemax[k]; j++){      }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    fprintf(ficrescveij,"\n");
            h++;    
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    if(estepm < stepm){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      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
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);     * if stepm=24 months pijx are given only every 2 years and by summing them
       codtab[1][2]=1;codtab[2][2]=2; */     * we are calculating an estimate of the Life Expectancy assuming a linear 
    /* for(i=1; i <=m ;i++){     * progression in between and thus overestimating or underestimating according
       for(k=1; k <=cptcovn; k++){     * to the curvature of the survival function. If, for the same date, we 
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       }     * to compare the new estimate of Life expectancy with the same linear 
       printf("\n");     * hypothesis. A more precise result, taking into account a more precise
       }     * curvature will be obtained if estepm is as small as stepm. */
       scanf("%d",i);*/  
        /* For example we decided to compute the life expectancy with the smallest unit */
    /* Calculates basic frequencies. Computes observed prevalence at single age    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        and prints on file fileres'p'. */       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 */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       survival function given by stepm (the optimization length). Unfortunately it
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       means that if the survival funtion is printed only each two years of age and if
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       results. So we changed our mind and took the option of the best precision.
          */
     /* For Powell, parameters are in a vector p[] starting at p[1]    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */  
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     if(mle==1){    agelim=AGESUP;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
     /*--------- results files --------------*/    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     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);    
      p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    jk=1;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    gp=matrix(0,nhstepm,1,nlstate*nlstate);
    for(i=1,jk=1; i <=nlstate; i++){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)    for (age=bage; age<=fage; age ++){ 
          {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
            printf("%d%d ",i,k);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
            fprintf(ficres,"%1d%1d ",i,k);      /* if (stepm >= YEARM) hstepm=1;*/
            for(j=1; j <=ncovmodel; j++){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);      /* If stepm=6 months */
              jk++;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
            }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
            printf("\n");      
            fprintf(ficres,"\n");      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
  if(mle==1){         decrease memory allocation */
     /* Computing hessian and covariance matrix */      for(theta=1; theta <=npar; theta++){
     ftolhess=ftol; /* Usually correct */        for(i=1; i<=npar; i++){ 
     hesscov(matcov, p, npar, delti, ftolhess, func);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
  }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        }
     printf("# Scales (for hessian or gradient estimation)\n");        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
      for(i=1,jk=1; i <=nlstate; i++){        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       for(j=1; j <=nlstate+ndeath; j++){    
         if (j!=i) {        for(j=1; j<= nlstate; j++){
           fprintf(ficres,"%1d%1d",i,j);          for(i=1; i<=nlstate; i++){
           printf("%1d%1d",i,j);            for(h=0; h<=nhstepm-1; h++){
           for(k=1; k<=ncovmodel;k++){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
             printf(" %.5e",delti[jk]);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             fprintf(ficres," %.5e",delti[jk]);            }
             jk++;          }
           }        }
           printf("\n");       
           fprintf(ficres,"\n");        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 */
     k=1;      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      
     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");      for(h=0; h<=nhstepm-1; h++)
     for(i=1;i<=npar;i++){        for(j=1; j<=nlstate*nlstate;j++)
       /*  if (k>nlstate) k=1;          for(theta=1; theta <=npar; theta++)
       i1=(i-1)/(ncovmodel*nlstate)+1;            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);       for(ij=1;ij<=nlstate*nlstate;ij++)
       printf("%3d",i);        for(ji=1;ji<=nlstate*nlstate;ji++)
       for(j=1; j<=i;j++){          varhe[ij][ji][(int)age] =0.;
         fprintf(ficres," %.5e",matcov[i][j]);  
         printf(" %.5e",matcov[i][j]);       printf("%d|",(int)age);fflush(stdout);
       }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficres,"\n");       for(h=0;h<=nhstepm-1;h++){
       printf("\n");        for(k=0;k<=nhstepm-1;k++){
       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++)
     while((c=getc(ficpar))=='#' && c!= EOF){            for(ji=1;ji<=nlstate*nlstate;ji++)
       ungetc(c,ficpar);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       fgets(line, MAXLINE, ficpar);        }
       puts(line);      }
       fputs(line,ficparo);  
     }      /* Computing expectancies */
     ungetc(c,ficpar);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     estepm=0;      for(i=1; i<=nlstate;i++)
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        for(j=1; j<=nlstate;j++)
     if (estepm==0 || estepm < stepm) estepm=stepm;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     if (fage <= 2) {            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
       bage = ageminpar;            
       fage = agemaxpar;            /* 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(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(ficresstdeij,"%3.0f",age );
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      for(i=1; i<=nlstate;i++){
          eip=0.;
     while((c=getc(ficpar))=='#' && c!= EOF){        vip=0.;
     ungetc(c,ficpar);        for(j=1; j<=nlstate;j++){
     fgets(line, MAXLINE, ficpar);          eip += eij[i][j][(int)age];
     puts(line);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     fputs(line,ficparo);            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]) );
   ungetc(c,ficpar);        }
          fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      fprintf(ficresstdeij,"\n");
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
            fprintf(ficrescveij,"%3.0f",age );
   while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);        for(j=1; j<=nlstate;j++){
     fgets(line, MAXLINE, ficpar);          cptj= (j-1)*nlstate+i;
     puts(line);          for(i2=1; i2<=nlstate;i2++)
     fputs(line,ficparo);            for(j2=1; j2<=nlstate;j2++){
   }              cptj2= (j2-1)*nlstate+i2;
   ungetc(c,ficpar);              if(cptj2 <= cptj)
                  fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      fprintf(ficrescveij,"\n");
      
   fscanf(ficpar,"pop_based=%d\n",&popbased);    }
   fprintf(ficparo,"pop_based=%d\n",popbased);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   fprintf(ficres,"pop_based=%d\n",popbased);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     ungetc(c,ficpar);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fgets(line, MAXLINE, ficpar);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);    printf("\n");
     fputs(line,ficparo);    fprintf(ficlog,"\n");
   }  
   ungetc(c,ficpar);    free_vector(xm,1,npar);
     free_vector(xp,1,npar);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
 while((c=getc(ficpar))=='#' && c!= EOF){  /************ Variance ******************/
     ungetc(c,ficpar);  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[])
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    /* Variance of health expectancies */
     fputs(line,ficparo);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   }    /* double **newm;*/
   ungetc(c,ficpar);    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    int movingaverage();
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double **dnewm,**doldm;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int k;
     double *xp;
 /*------------ gnuplot -------------*/    double **gp, **gm;  /* for var eij */
   strcpy(optionfilegnuplot,optionfilefiname);    double ***gradg, ***trgradg; /*for var eij */
   strcat(optionfilegnuplot,".gp");    double **gradgp, **trgradgp; /* for var p point j */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    double *gpp, *gmp; /* for var p point j */
     printf("Problem with file %s",optionfilegnuplot);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   }    double ***p3mat;
   fclose(ficgp);    double age,agelim, hf;
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    double ***mobaverage;
 /*--------- index.htm --------*/    int theta;
     char digit[4];
   strcpy(optionfilehtm,optionfile);    char digitp[25];
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    char fileresprobmorprev[FILENAMELENGTH];
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }    if(popbased==1){
       if(mobilav!=0)
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        strcpy(digitp,"-populbased-mobilav-");
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      else strcpy(digitp,"-populbased-nomobil-");
 \n    }
 Total number of observations=%d <br>\n    else 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      strcpy(digitp,"-stablbased-");
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li>Parameter files<br>\n    if (mobilav!=0) {
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   fclose(fichtm);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
  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);    strcpy(fileresprobmorprev,"prmorprev"); 
      sprintf(digit,"%-d",ij);
  free_ivector(wav,1,imx);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
  free_ivector(num,1,n);    strcat(fileresprobmorprev,fileres);
  free_vector(agedc,1,n);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      printf("Problem with resultfile: %s\n", fileresprobmorprev);
  fclose(ficparo);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
  fclose(ficres);    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   /*--------------- Prevalence limit --------------*/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      pstamp(ficresprobmorprev);
   strcpy(filerespl,"pl");    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);
   strcat(filerespl,fileres);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      fprintf(ficresprobmorprev," p.%-d SE",j);
   }      for(i=1; i<=nlstate;i++)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   fprintf(ficrespl,"#Prevalence limit\n");    }  
   fprintf(ficrespl,"#Age ");    fprintf(ficresprobmorprev,"\n");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficgp,"\n# Routine varevsij");
   fprintf(ficrespl,"\n");    /* 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");
   prlim=matrix(1,nlstate,1,nlstate);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*   } */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficresvij);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    if(popbased==1)
   k=0;      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);
   agebase=ageminpar;    else
   agelim=agemaxpar;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   ftolpl=1.e-10;    fprintf(ficresvij,"# Age");
   i1=cptcoveff;    for(i=1; i<=nlstate;i++)
   if (cptcovn < 1){i1=1;}      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresvij,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;    xp=vector(1,npar);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficrespl,"\n#******");    doldm=matrix(1,nlstate,1,nlstate);
         for(j=1;j<=cptcoveff;j++)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficrespl,"******\n");  
            gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         for (age=agebase; age<=agelim; age++){    gpp=vector(nlstate+1,nlstate+ndeath);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    gmp=vector(nlstate+1,nlstate+ndeath);
           fprintf(ficrespl,"%.0f",age );    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           for(i=1; i<=nlstate;i++)    
           fprintf(ficrespl," %.5f", prlim[i][i]);    if(estepm < stepm){
           fprintf(ficrespl,"\n");      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 */
   fclose(ficrespl);    /* 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 
   /*------------- h Pij x at various ages ------------*/       nstepm is the number of stepm from age to agelin. 
         Look at function hpijx to understand why (it is linked to memory size questions) */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if((ficrespij=fopen(filerespij,"w"))==NULL) {       survival function given by stepm (the optimization length). Unfortunately it
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       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 
   printf("Computing pij: result on file '%s' \n", filerespij);       results. So we changed our mind and took the option of the best precision.
      */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   /*if (stepm<=24) stepsize=2;*/    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   agelim=AGESUP;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   hstepm=stepsize*YEARM; /* Every year of age */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   k=0;      gp=matrix(0,nhstepm,1,nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){      gm=matrix(0,nhstepm,1,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");      for(theta=1; theta <=npar; theta++){
         for(j=1;j<=cptcoveff;j++)        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         fprintf(ficrespij,"******\n");        }
                hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        if (popbased==1) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if(mobilav ==0){
           oldm=oldms;savm=savms;            for(i=1; i<=nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                prlim[i][i]=probs[(int)age][i][ij];
           fprintf(ficrespij,"# Age");          }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)            for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)              prlim[i][i]=mobaverage[(int)age][i][ij];
               fprintf(ficrespij," %1d-%1d",i,j);          }
           fprintf(ficrespij,"\n");        }
            for (h=0; h<=nhstepm; h++){    
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        for(j=1; j<= nlstate; j++){
             for(i=1; i<=nlstate;i++)          for(h=0; h<=nhstepm; h++){
               for(j=1; j<=nlstate+ndeath;j++)            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
             fprintf(ficrespij,"\n");          }
              }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* This for computing probability of death (h=1 means
           fprintf(ficrespij,"\n");           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++)
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   fclose(ficrespij);        /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   /*---------- Forecasting ------------------*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if((stepm == 1) && (strcmp(model,".")==0)){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);   
   }        if (popbased==1) {
   else{          if(mobilav ==0){
     erreur=108;            for(i=1; i<=nlstate;i++)
     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);              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   /*---------- Health expectancies and variances ------------*/          }
         }
   strcpy(filerest,"t");  
   strcat(filerest,fileres);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   if((ficrest=fopen(filerest,"w"))==NULL) {          for(h=0; h<=nhstepm; h++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          }
         }
         /* This for computing probability of death (h=1 means
   strcpy(filerese,"e");           computed over hstepm matrices product = hstepm*stepm months) 
   strcat(filerese,fileres);           as a weighted average of prlim.
   if((ficreseij=fopen(filerese,"w"))==NULL) {        */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
  strcpy(fileresv,"v");        /* end probability of death */
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        for(j=1; j<= nlstate; j++) /* vareij */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          for(h=0; h<=nhstepm; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          }
   calagedate=-1;  
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      } /* End theta */
       k=k+1;  
       fprintf(ficrest,"\n#****** ");      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(h=0; h<=nhstepm; h++) /* veij */
       fprintf(ficrest,"******\n");        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
       fprintf(ficreseij,"\n#****** ");            trgradg[h][j][theta]=gradg[h][theta][j];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       fprintf(ficreseij,"******\n");        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
       fprintf(ficresvij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficresvij,"******\n");      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          vareij[i][j][(int)age] =0.;
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        for(h=0;h<=nhstepm;h++){
          for(k=0;k<=nhstepm;k++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       oldm=oldms;savm=savms;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);          for(i=1;i<=nlstate;i++)
                for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    
       fprintf(ficrest,"\n");      /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       epj=vector(1,nlstate+1);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(age=bage; age <=fage ;age++){      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         if (popbased==1) {          varppt[j][i]=doldmp[j][i];
           for(i=1; i<=nlstate;i++)      /* end ppptj */
             prlim[i][i]=probs[(int)age][i][k];      /*  x centered again */
         }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
              prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         fprintf(ficrest," %4.0f",age);   
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      if (popbased==1) {
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        if(mobilav ==0){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];          for(i=1; i<=nlstate;i++)
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/            prlim[i][i]=probs[(int)age][i][ij];
           }        }else{ /* mobilav */ 
           epj[nlstate+1] +=epj[j];          for(i=1; i<=nlstate;i++)
         }            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
         for(i=1, vepp=0.;i <=nlstate;i++)      }
           for(j=1;j <=nlstate;j++)               
             vepp += vareij[i][j][(int)age];      /* This for computing probability of death (h=1 means
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         for(j=1;j <=nlstate;j++){         as a weighted average of prlim.
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      */
         }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         fprintf(ficrest,"\n");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     }      }    
   }      /* end probability of death */
 free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     free_vector(weight,1,n);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   fclose(ficreseij);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   fclose(ficresvij);        for(i=1; i<=nlstate;i++){
   fclose(ficrest);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   fclose(ficpar);        }
   free_vector(epj,1,nlstate+1);      } 
        fprintf(ficresprobmorprev,"\n");
   /*------- Variance limit prevalence------*/    
       fprintf(ficresvij,"%.0f ",age );
   strcpy(fileresvpl,"vpl");      for(i=1; i<=nlstate;i++)
   strcat(fileresvpl,fileres);        for(j=1; j<=nlstate;j++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        }
     exit(0);      fprintf(ficresvij,"\n");
   }      free_matrix(gp,0,nhstepm,1,nlstate);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   k=0;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    } /* End age */
       k=k+1;    free_vector(gpp,nlstate+1,nlstate+ndeath);
       fprintf(ficresvpl,"\n#****** ");    free_vector(gmp,nlstate+1,nlstate+ndeath);
       for(j=1;j<=cptcoveff;j++)    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       fprintf(ficresvpl,"******\n");    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 */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       oldm=oldms;savm=savms;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  /*   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));
   fclose(ficresvpl);    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));
   /*---------- End : free ----------------*/    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);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
    */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    
      free_vector(xp,1,npar);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(doldm,1,nlstate,1,nlstate);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(dnewm,1,nlstate,1,npar);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(matcov,1,npar,1,npar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_vector(delti,1,npar);    fclose(ficresprobmorprev);
   free_matrix(agev,1,maxwav,1,imx);    fflush(ficgp);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    fflush(fichtm); 
   }  /* end varevsij */
   fprintf(fichtm,"\n</body>");  
   fclose(fichtm);  /************ Variance of prevlim ******************/
   fclose(ficgp);  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 */
   if(erreur >0)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     printf("End of Imach with error or warning %d\n",erreur);  
   else   printf("End of Imach\n");    double **dnewm,**doldm;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    int i, j, nhstepm, hstepm;
      double *xp;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    double *gp, *gm;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    double **gradg, **trgradg;
   /*------ End -----------*/    double age,agelim;
     int theta;
     
  end:    pstamp(ficresvpl);
 #ifdef windows    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   /* chdir(pathcd);*/    fprintf(ficresvpl,"# Age");
 #endif    for(i=1; i<=nlstate;i++)
  /*system("wgnuplot graph.plt");*/        fprintf(ficresvpl," %1d-%1d",i,i);
  /*system("../gp37mgw/wgnuplot graph.plt");*/    fprintf(ficresvpl,"\n");
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    xp=vector(1,npar);
  strcpy(plotcmd,GNUPLOTPROGRAM);    dnewm=matrix(1,nlstate,1,npar);
  strcat(plotcmd," ");    doldm=matrix(1,nlstate,1,nlstate);
  strcat(plotcmd,optionfilegnuplot);    
  system(plotcmd);    hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
 #ifdef windows    agelim = AGESUP;
   while (z[0] != 'q') {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     /* chdir(path); */      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      if (stepm >= YEARM) hstepm=1;
     scanf("%s",z);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     if (z[0] == 'c') system("./imach");      gradg=matrix(1,npar,1,nlstate);
     else if (z[0] == 'e') system(optionfilehtm);      gp=vector(1,nlstate);
     else if (z[0] == 'g') system(plotcmd);      gm=vector(1,nlstate);
     else if (z[0] == 'q') exit(0);  
   }      for(theta=1; theta <=npar; theta++){
 #endif        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__) 
   #include <gnu/libc-version.h>  /* Only on gnu */
      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
      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
      
   
    }
   
   /***********************************************/
   /**************** 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 */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       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.1.47  
changed lines
  Added in v.1.178


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